PC:
RPGs: Planescape:Torment - Most intelligent and deep dialogue/story in a game EVER. A story you still think about after you beat the game, not to mention HILARIOUS voice acting/dialogue and unforgettable characters. If a Final Fantasy game is a good movie, this game is a good book. This game was adapted from a novel, and features very complex/adult ideas, themes....everything from spirituality to conspiracy theories to personal responsibility, etc. Not to mention your main friend in the game is a floating, talking skull.
Elder Scrolls:Arena.
Elder Scrolls

aggerfall (fuck morrowind wack ass game)
Might and Magic VI - Those old school RPGs in 3d where you had your party faces on the bottom are tight - This one was the best of them all.
Non-RPGs:
Half-Life - amazing use of story and atmosphere in an FPS. This shit will definitely stand the test of time.
X-Com: UFO Defense - You can not knock this game in any way, shape or form. This shit was tight as Fuck.
First Diablo - Great music, theme, atmosphere. An RPG where you don't have to think about much.
MechWarrior 2:Mercenaries - Good ass graphics, choices to betray people, and the ability to make and customize your own little tank army. This shit was way ahead of its time.
Genesis:
Shadowrun - Cyberpunk American-style RPG where you can do what you want, hack computers, break into corporations, etc. This shit went under the radar because the first 20 hours of play you have to do extremely repetitive quests to get where you have enough money to go somewhere, but the ability to buy illegal guns/grenades/armor, kill cops or put them on your payrolll, join the Mafia or Yakuza, get mods on your body, choose who you want to hire on your team, etc., all beneath a sick ass Cyberpunk-style storyline in a futuristic world. Classic.
GunStar Heroes - Simple, Fun, Fun two player
Shining Force / Shining Force 2 / Shining in the darkness - Japanese Strategy/RPG...Very fun, great storyline, very customizable characters...combat was a blast...etc.
X-Men - Great graphics...fun to play, etc.