dataDyne Defection:

The Sitting Deadlikes: Sneak up on a sitting guard, and shoot him with the Psychosis Gun. He will of course get up, and start shooting his comrades. But when you kill him, he will be in the sitting position! This is a still screenshot, not an action one. He is frozen this way. 

Cassandra's Two Necklaces: If you are fast enough to punch Cassandra DeVries, and jump back without collecting her keycode necklace, she will still be wearing it, AND, it will be available on the ground for you to pick up. It's visible here right by her feet, AND she is also wearing it...

Unconscious Conversation: You can make Cassandra DeVries speak while she's been knocked out, and on the floor.
With the Enemy Shields cheat, punch out Cassandra. She'll fall to the ground as usual, but she'll keep talking. Quite odd to see someone threatening you while they've been KO-ed...

dataDyne Investigation:

Double CMP150s: You must not be seen for this one. Time it so that the patrolling guard at the start of the level is past the elevator when you exit it. Head down the hall, where the cleaning bot opens the passage. Shoot the glass at the bottom of the ramp to get down. Sneak around the corner, and hopefully the guard will have his back turned, or will not be in sight. You can grab two CMP150s in these holds, between the cleaning bot control computers. 

dataDyne Extraction:

DY357 Magnum: If your aim is Perfect, and you pick off the first five guards on the ground level with perfect head shots, the fifth and final one will be carrying a DY357 Magnum. 

Cassandra's Keycard, Grenade & Dragon: If you reach the upstairs by killing ALL guards before they fire a single shot, or by using the Cloaking Device Cheat, a guard will appear after you exit the elevator, and will drop Cassandra's Keycard. The Key opens the office, where a grenade is on her desk, and a secret passage behind a blown wall, where a Dragon is found.

Cinema Scene Characters: An addition to the trick above, after getting Cassandra's office keycard, you can head downstairs, to where the external comms hub is, the door will now be unlocked. Inside, are two female guards, and Mr. Blonde, standing motionless. There are also two Rockets. You can't kill the characters, only paint them red with blood, and the blood will show up in the cinema scene. Also with the keycard, you can unlock the door to the highway on this same ground floor.

Blinded Female Guards: After you meet up with Cassandra DeVries, the lights go out, and her guards with shotguns attack you. But if you hit the light switch near the entrance to the room, they will be momentarily blinded, as they are set for "night vision". Cool detail.

Kill Dr. Caroll, finish mission: Another effect of getting the keycard, allows you to pick up the Dragon hidden behind Cassandra's office. Complete all other objectives, and head for the helipad. Throw the Dragon as a proximity detonator onto the helipad, and step on. Dr Caroll will explode, and the cinema scene kicks in, without Dr. Caroll.

Rocket Guards: Turn on the Enemy Rockets cheat, and complete dataDyne Extraction, or simply watch the Cinema scene "Going Somewhere?" from the menu. Cassandra's two bodyguards will of course be armed with Rocket Launchers, but when they fire, the effects are that of their usual Shotguns, but they sound like Rockets, with no explosions.

Carrington Villa:

Strange Negotiation: Something interesting happens here while using the 'Marquis of Queensbury Rules' (Enemies without weapons) Cheat.

Playing on Secret Agent difficulty, you can head down to the docks, and see the guards with the negotiator. They have no weapons, so they can't shoot and kill her. They remain frozen in place, and won't even respond to you. Once you kill them, the negotiator will run as usual. You can follow the negotiator, and watch her disappear into thin air when she goes around the corner of the building.

Double CMP150s: If you manage to reach this Sniper, and eliminate him 38 seconds into the mission or less, two CMP150s are found by his corpse when he hits the ground. It's practically impossible to do on Perfect Agent, unless you cheat.

Devastator: Just past the Sniper listed above, is a clearing. Three crates are off to the side. There are a pair of crates, and another one beside them. Blow up the lone crate to expose a Devastator, hidden inside. 

Carrington Scolding: Daniel Carrington is being held captive in his own villa's own basement. In the basement, are many liquor bottles on cases. Destroy every last one of them, and you'll hear Carrington say "Act your age, Joanna". Cool little thing for the programmers to throw in, for anyone adventurous (and destructive) enough to destroy all the bottles. 

Chicago Stealth:

BombSpy: In the opening of the level's central alley, there is a trash bin, and some explosive barrels. Push the trash bin on an angle, so it is beside the barrels. Stand back, and blow up the barrels, to release the BombSpy from the trash bin. The bomb spy can be used on the guards guarding the carport, to create an alternate diversion, instead of using the taxi. 

Pond Punk; Double Falcons: Right in front of the limousine, the building's door is unlocked. You can enter, and head down the stairs. Guards await down there, and there is a locked door. Guards may get up from inside to unlock the door, or you can disarm a guard, who will then run and open the door. Inside is a large tavern, with a bar, stools, and even a can. Double Falcon 2s are on the bar, waiting to be picked up by you.

Reusable Mine, Counter-Operative: Joanna only has one mine to throw on the blocked up doors, for an escape route. But after she throws it, have her again choose her Remote Mines, which are now at zero. When the Counter-Operative player disarms her, she can pick up the Remote Mine off the ground, and once again have a mine to reuse. If you shoot the mine that you placed on the door, you'll fail the mission, even if you place another one in it's place.

G5 Building:

Crossbow: After shooting one guard dead in the level's very first room, where you start, knock the other one out with Pistol Whip, or your fists. He will drop a Crossbow once he goes down.

Floating Guard Guns: Complete all your objectives, and once the alarm goes off after planting the door decoder on the safe, head back to the stairs where you reached that floor. On the highest part of that set of stairs, shoot and kill a guard who is on the stairs themselves. Their weapon will float upwards, to the ceiling, then appear on the ground.

Area 51 Infiltration

Find Jonathan Before Cinema Scene: As in Goldeneye, you can get guards to open locked doors by shooting, and running around the door while Invisible. In this case, while Cloaked. After leaving the surface, and entering the first hangar, get the guards to open the large door by the ramp this way. Once opened, you can explore part of the next level's starting, with a missing lift that you can jump down, and Jonathan with the guard he shoots in the Cinema scene. You can't kill either, but you can shoot their guns from their hands, and use them yourselves. This is a really cool trick.

Area 51 Rescue:

Long trek to a Phoenix: Once heading up the levels first lift, head right, down the hall, to the lone guard in front of a locked door. If you shoot the guard with the Psychosis gun, he'll open it. Or, if you did not kill the Overalls guard in the previous mission, he will open it for you after you get the locked door message. You are in an empty hangar, where you head up in another lift, through a whole bunch of doors and twists, and end up overlooking the helipad outside. Right there, is a Phoenix. Cool.

Area 51 Escape:

Double Falcons: Only a fool would remain in a room filling with gas... But the actual operating room itself, where the gassed biotechnicians were, has two Falcons from their dead bodies for you to snatch before you leave.

Remote Mines: If you push the alien on the hovering stretcher to your destination point in under 31 seconds, 3 Remote Mines will be waiting for you after passing through the circular room with the biotechnicians, and through the next door, into the small hall. The same room where Jonathan will set the explosives. 

From the Nintendo Power Players Guide 

'Invisible' Elvis: At the start of the level, use the trick to kill the distant, standing Elvis with your FarSight (see Solved Mysteries section for details). After killing this Elvis, proceed through the level, and start the cinema scene where Elvis awakes. He won't physically be there, you'll only hear his voice. Cool.

Air Base Espionage:

Floating, Twirling Weapons: Inside the first room of the air base itself, look up, to see this big, glass window. Shoot a few crossbow bolts into it, then blow it up with your Rocket Launcher. The bolts will fall down, and will forever twirl around inches off the ground. Same goes for enemy guns. Cool.

Crash Site Confrontation:

DY357-LX: Trent Easton is always armed with his DY357-LX, and the same goes for whenever he is holding the President at gunpoint. It's possible to disarm him, and grab it as he runs by, after you save the President. But it's easier to sneak up while cloaked, and disarm him. The President will not leave the level with you if you do it this way though.

Pelagic II:

Double Falcons: If you manage to reach the area with the second alarm, and kill all the guards there without having one of them trigger the alarm, one will drop double Falcons for you to pick up.

Elvis Glitch: Elvis always gives you instructions at the start of the level. But if you shoot him with the Psychosis gun at any time, even after he's finished talking, he'll repeat his lines over again.

CI Defense:

Devastating Save: In the upstairs area of the Carrington Institute, you must save four hostages in two offices. If you can save the lives of all four of them, the last hostage will leave behind a devastator for you. This can be tricky to do, so using the Combat Boost is your best bet.

Attack Ship:

Cassandra Not Killed: Many characters behave strangely when shot with the Psychosis Gun. But in this level, if you hurry and start, and shoot Cassandra before she disappears, she'll freeze in place. This is done much easier with Slo-Mo turned ON. She just stands there... If you put your crosshairs on her, the target box turns red, indicating she's an enemy. On Perfect Agent, she of course drops her necklace when you decide to kill her.

Skedar Ruins:

Double Phoenix: The level has five pillars, and only a random three of them will need to be marked with a Target Amplifier. If you destroy the ones that aren't marked on the radar, you will find two Phoenix pistols at the rubble of the second useless pillar. This makes beating the Skedar leader much easier... And much more entertaining.

Combat Training:

Training for Murder: On the target range, you can block the door, so it won't close. You can then choose any weapon, and fire it at the technicians there. They can't be killed, but knives, arrows, and mines stick to them. You can also fly Slayer Rockets around there, and if you're quick enough, out the door and through the entire Institute.

Shoot out Goldeneye Weapons: With the FarSight XR-20, you can pick off the individual classic weapons from Goldeneye that are in the display cases. They fall right through the ground, and when you leave the range, they're missing.

Use Knives on Technicians: This is a cool, but complicated trick to perform. In the CI, head down to the hangar, and find the hovercrate that's near a technician. Push it all the way upstairs, into the firing range. Select a firing session with Knives, and throw as many as you can into the crate.

End the session, and take the crate upstairs, to where two technicians are, in the device training room. Go back to the firing range, select the FarSight, and look through the right wall, and up, to blow up the crate. Head back up to the device training room, and knives will be scattered all along the ground. Try to avoid picking up any knives. Select any device from the device training, and pick it up off the table. You can then pick up knives, and use them in the session!

Combat Simulator:

BEAT (cheat) CHALLENGES, YOU CALL THE SHOTS: Head to the Advanced Setup, with at least two players. One player chooses the Settings option, to load a previously saved setup, one that is easy to win at. Stay at that screen, and do not select a setting yet. The second player chooses a challenge from the challenger menu, and prepares to start the game. The first player then selects the preset challenge. Start the game, and when you win, you are credited for beating that challenge. The simplest setup, is to have a few Meat Sims against you, with a few more difficult Sims on your side, for a minute of play.

Absolute Kill Master: There is a very easy way to score Multiple kills, after setting it up, you can just sit back and relax as your kill count racks up.

In the Felicity, your case must be in the bathroom. If not, restart until you begin there. Capture the Case, with Remote Mines, and 8 Simulants on your team. Get at least three Simulants into the small starting room, plant a mine on the wall or ceiling, and another mine on a sim. Get out of the way, and detonate. The explosions will continue, again and again, earning you more and more kills. Some Simulants may not have been killed initially, so kill them, so they'll reappear in the room as well, to be killed instantly. You don't need to do anything now, just find a safe place, and quit whenever your kill count is as desired. I've gotten 3000 kills in ten minutes. Just don't get caught in the explosion, or else you won't be able to press start to end your game, and save your stats, unless you preset a limit time.

Truthful Kill Master: It is entirely possible to pull of the trick above, when the 8 Simulants are not on your team. To do this, their team must have their case in the bathroom. It's harder to do, since you can't control the Sims, but once you manage to get the explosion cycle going, it works. Don't be afraid to accidentally kill yourself attempting to blow up three Sims at once. If you die in the mass explosion, you will reappear safe in your own base, while the others face eternal death.

Floating Ammo: The first glitch in Perfect Dark that I actually discovered. Completely useless of course, but just fun to do. Collect any ammo box while it's still in the air, after being shot. When it reappears, it will be where it was when you picked it up. Shoot it again to make it fall back down.

Mines on players: Sounds so stupid, who would have actually tried it? If you throw any kind of mine on a player, it will stick right to them. That's got to be quite a feeling... You have a bomb on you, and know it will explode at any moment.

Double Knife Death: After a player dies, you can throw poison tipped knives at their dead body on the ground. Those knives will be there when they reappear, and will more than likely kill them again. Nasty.

Weapon Glitch: In a 2 player match, have one player kill the other, and then pause the game. The 'killed' player can now press START, and bring up his weapon screen, and attempt to select a weapon, even though he's dying. Keep selecting the weapon with 'A', and have the other player unpause the game, while 'A' is still being pressed. When the player returns to life, his weapons screen will still be there, with Unarmed, but a description of the weapon he previously chose. Weird.

Counter-Operative:

Restarting: If the "bad guy" human player in Counter-Operative gets killed, and every other available enemy for them to control has also been killed, they will of course, start unarmed, at the level's starting point. But if Joanna is around to watch them appear, they tilt, and seem to grow right out of the ground. Cool.

Misc:

Maximize and extend RC-P120 cloaking: The cloaking function of the RC-P120 is very useful, but it's also a major drain on your ammo. There is a way to greatly maximize the use of your ammo for cloaking though.

Use the RC-P120 to cloak as normal. Just as it has almost drained your clip, press and hold the trigger. This should cause you to uncloak, and then cloak again. You'll now be cloaked, and not using any ammo.

You will eventually uncloak after a few minutes, and you may need to switch to another weapon, and then switch back before you can use the RC-P120 again.

Portable Laptop Gun: A basic knowledge trick, but anyway... After throwing a Laptop Gun as a Sentry Gun, it clears out the enemies in that area. But you haven't thrown it away forever, just approach it, and press "B" to pick it up again.

Reuse Crossbow Bolts: If you miss an enemy with the crossbow, you can always find the bolt, and pick it up to reuse it. But if you hit the enemy, he falls, and the bolt stays in him. But you can use a gun, and shoot the bolt out of him, and pick it up.

X-Rayted Cinema: If you complete any level while having the X-Ray scan activated, the cinema scene will be seen in X-ray vision. The same effect also happens if you exit a level using the Night Vision Goggles.

Invisible Jo: Basically the same as above, but if you exit a level while Joanna is cloaked, she will also be cloaked in the cinema scene.

FarSight Vision: There are a few levels that end that you don't have to exit through a door. Crash Site, Skedar Ruins... If you are looking through your FarSight's scope when the level ends, the cinema scene will be seen as if looking through the FarSight. Here's Trent Easton pulling out his DY-357 LX against Mr. Blonde.

Charred Black: This only works for the first few guards you kill in a level. Punch someone out, or pistol whip them. Next, shoot them with an explosive blast, and they will almost die for a second time, only now, their corpse will be charred black.