Some that stand out in my memory:
QuakeWorld Capture the Flag and Team Fortress. Before that all we knew was mindlessly fragging eachother in deatmatch. I think it was a huge departure for multiplayer FPS games.
Netstorm: Islands at War, a multiplayer RTS game with floating islands in the sky with a unique style that succesfully combined a puzzle game element of building bridges with random pieces to reach other islands or to block incoming enemies.
I'm surprised that there hasn't been anything like it when this combination worked so incredibly well.
Dungeon Keeper, I think managing a dungeon, underground digging & destroying heroes is one of the coolest & most fun game concepts.
Fallout 1 & 2, I think these are most immersive games I've played. The unique setting, gritty atmosphere and dialogues really sucked me in. I also thought isometric turn-based combat and selection of firearms was really cool.
Ultima Online, my first MMO experience, there was nothing like it.
most recently:
Holy Invasion of Privacy Badman, What Did I Do to Deserve This?
Arcade style dungeon management based on an ecosystem. Wow!