What a question... There are so many. I never get tired or plaything these games. I still own and play the games and their consoles. Wish I had the arcade cabinets though.
Nes:
Indiana Jones and the Last Crusade (Taito)
Contra
Punch out!
SNES:
Super Punch Out!
Jimmy Houstins Bass Tournament USA
Super Black Bass
The Legend of Zelda: A link to the past
Killer Instinct
Super star wars
Indiana Jones Greatest adventures
N64:
Goldenye
Ocarina of Time
Game Cube:
Resident evil 4
Metalgear solid: The twin snakes
PS1:
Metal Gear solid
Resident evil 2
Dragonball Z: Greatest Legends (Jap import)
Dragonball GT Final Bout (Both versions)
PS2:
Metal Gear Solid 2 & 3
PS3:
Metal Gear Solid 4
Mortal Kombat II
Cod MW & MW2
Xbox:
Ninja Gaiden
Shenmue II
Max Payne 1&2
Dreamcast:
Shenmue
Resident Evil: Code Veronica
Arcade:
Mortal Kombat 1&2
Star Wars Trilogy Arcade
Killer Instinct
Zombies Ate My Neighbors
Revolution X
Sim City
Full Throttle
Freedom Force
Half-Life
Half-Life 2
Enter The Matrix
Portal
Tron 2.0
The Sims 2
The Great Escape
Grand Theft Auto: San Andreas
Left 4 Dead
Killing Floor
Ghostbusters: The Video Game
Zelda ocarina of Time
Zelda Majora's Mask
Scrolls of Oblivion (xbox 360) : I spent over 60 hours of playing this game. Great value for the price.
Call of Duty Modern Warfare
Gears of War
MARIO 64
MARIO KART 64
I love the original stand-up Star Wars vector game. The uniqueness of teh controller for it was part of the reason I loved it so much. Playing it on other platforms just is never the same. I'd love to find one and buy it for my home.
I really, really miss playing Marathon on the Mac back in the early 90's.
My best memories are of playing Quake 3 over the LAN network where I worked in 2000. That was the peak of my gaming experience partially because of the environment.
I also was really impressed with Portal. Pretty amazing game.