1999 Aliens vs. Predaror had:

• actual 3D waves. The mesh for the water surface was actually transformed and reacted to your character moving through it creating waves—you could slosh the whole small pools around by running around in them. No shader trickery there.
• explosion fireballs that were 3D and freaking reacted to the environment. Throw a grenade on the floor, the fireball is hemispherical. Throw in into a ventilation shaft, you get a pillar of fire shooting out from the opening. It was absolutely mind-blowing!
• physics engine that allowed physics-enabled objects to be thrown around, bouncing from the walls etc. In 1999. Bizarrely, the objects couldn't rotate so they always retained the same orientation. It saw use in level design where you could destroy the supports of some stone blocks and let them fall down to block some large pipes.
• flame thrower flame reflected from the walls. You could shoot around a corner or set yourself on fire in confined spaces with it.
• no apparent limit for texture resolution. I remember people modding it with 1k and 2k textures (originals were like 64x64 or 128x128). In 2002.