I've never been able to get the Grays out of their radiation chamber. Even if they're after me, they always seem to wait just inside the door instead of coming out.
That MIB with the assault rifle nearby behaves a bit strangely. He is usually the first one to attack the greasels and the bum, but he seems to only have a single 7.62mm clip and he just runs away from any fighting when he is out of ammo. He may occasionally run all the way to the soldier's quarters, where the troops consider him an enemy and kill him.

I think the best place for fooling around is actually the Paul Denton / UNATCO fight scene. A lot of strange things can happen during that. I once had Paul accidentally fall into the elevator shaft while he was fighting. Both he and the UNATCO troops could see each other but their guns weren't in each other's line of fire, so they were just standing there like statues, ready to fire. I tossed one of the comfy chairs into the shaft and it kept bouncing on Paul and hurting him (the walls of the shaft held it in place), so he became angry at me too.
He may also happen to step on the cleaner bot a bit later and quickly destroy it. You can see the same sort of the thing in the Vandenberg base, near the medical bot in the main building. The troops often hit it by mistake and then promptly blow it up.
I've kept savegames at all the funny points in the game, so I can always load one up whenever I need a few laughs.

DX Invisible War also has quite a few hilarious parts, mostly with the physics but also the AI. I had a savegame in Trier where all the civilians were afraid of a mouse and were cowering and/or running from it, but overwrote it by mistake.
In the Greasel Pit, in the room with the pool table, there is one bearded bum standing next to a plank-like object on the wall. If you keep bumping into that object, you can make it topple over and fall on the bum. When the bum starts walking around, the plank gets flung away in some direction at a very high speed.
In the Cairo ApostleCorp level, you can bring all the Templar bodies you find to the lobby (there are around 15 of them) and pile them up behind one of the sofas. If you put the utility cart on top of the pile it will bounce a couple of times and then get thrown off, taking several of the bodies with it.
I also like how the Illuminati commandos say "hmm...I am flammable!" when they catch on fire.

As for the ragdoll physics, pictures are worth a thousand words, although even they don't show all the vibrating motion and the bumping sounds:
http://home.comcast.net/~cp5670/ragdoll.jpghttp://home.comcast.net/~cp5670/ragdoll2.jpghttp://home.comcast.net/~cp5670/ragdoll3.jpghttp://home.comcast.net/~cp5670/ragdoll4.jpg