Plaupius on 16 February 2009
Few C64 games can truly stand the test of time, and it's quite obvious that graphics have nothing to do with it. Some great games have already been mentioned, so I'll just throw in my 2 cents, shamelessly repeating when necessary.
Internation Karate +
Ultima IV
Maniac Mansion
Paradroid
Monty on the Run & Auf Wiedersehen Monty (for the soundtrack)
The Great Giana Sisters (I know it's a Mario rip-off, but it's good anyway)
Wasteland
Stunt car Racer (one of, if not the best racing game ever)
Hitchhiker's Guide to the Galaxy (most probably the MOST RIDICULOUSLY DIFFICULT GAME EVER)
