It's a strange hobby, this arcade business. Practically all the games were difficult, bad graphics, and expensive to play. But I think that is aprt of the charm - easy to play, hard to master. And the battle for the high scores were legendary. Not to mention built out of unobtainium - they weren't games you could really "own", except for a crummy port to a home console.
The games I will remember on arcade vastly outnumber the home console games I think about from time to time. Console games are very much "in the moment" and when you are done with them, they seem to go away. Here's a few non-arcade games that I hold dear:
FFVII (PS)
Resident Evil 1 & 2 (PS)
Splinter Cell Chaos Theory (xbox)
Airborne Ranger (c64)
Maniac Mansion (c64)
Rainbow Six Three (PC version)
Racing Destruction Set (c64)
Paradroid (c64)
Wow... Racing Destruction Set and Paradroid... There's a blast from the past. My best friend and I used to play Racing Destruction Set and make all these outrageous tracks in low/high gravity just to watch our vehicles float off or pancake... Loved that game...

Rainbow Six Three (PC) was also a lot of fun, I think I played that one and R6 Vegas 2 (also PC) the most out of the series.
I do remember several C64 game that I loved:
Racing Destruction Set
Paradroid
Archon I & II
Uridium
Blue Max
Impossible Mission
Spy vs. Spy
Out of all the computers I've owned, I think I get the most nostalgic for the C64... I loved the Amiga also, but the C64 games we just awesome...

Other games that I have some very fond memories of are because of the ties to friends and my kids... Some of the best times I had gaming was with them...
Pro Wrestling (NES)
Battle Arena Toshinden (PSX)
Dragon's Lair and Space Ace (Arcade)
Street Fighter II and all variants (Arcade and console versions)
Super Smash Bros. (N64, played this with my daughters a lot)
Unreal Tournament 2K and 2K3 (PC, played with my kids and friends on many LAN parties)