Some of mine are probably going to date me as a fogey.
Borderlands: I second the chest-openning animation. Also the degree to which everyone is crazy as fuck. I wonder if Pandora has some weird geomagnetic field or something that messes with brains.
GTA III and Vice City the head and tail lights reflect in columns in the wet pavement. Sadly, the effect was forgotten in San Andreas
Also, in any sandbox game: birds.
Half Life: Opposing Force: Petting the spore launcher. That the spore launcher occasionally asks for pets.
Freedom Fighter: The joy your buddies express when they man a gun emplacement. Say hello to my little friend!
Left 4 Dead 2 Never-ending banter. I still hear bits that I hadn't heard before. Also, Ellis used to be infatuated with Zoey, but I think he's more smitten by Francis, or his true love, the Jimmy Gibbs.
Also, the graffiti!
Valve games in general: the ability to hotkey basic dialogue options. It helps keep a team cohesive to be able to say "Thank you", "I'm sorry" and "Good job!" with a keytap.
Star Wars: Republic Commando: I second the screen wiper, which clears oil, bug innards, rain and impact cracks.
Thief: The Dark Project: The first game (that I know) to allow leaning left, right and forward (makes peering over cliffs safer). Also, single-button controls for creep, walk and run. Having chorded sprint keys (especially when the sprint key doesn't chord with anything else but forward) has become a pet peeve of mine, but one I fix with hotkey software.
238U