Are we counting playthroughs from start to finish or games you've played for an extended perioid of time for 100 times or more? Since you listed Yar's revenge, a game with no ending (that I know of), I'm assuming the latter? If so;
Tony Hawk's Pro Skater 2, 3, 4, Underground 1, Underground 2
Warcraft 3
Runescape
Warhammer Online
Ape Escape
World of Warcraft
Day of Defeat Source
Half Life 2 Deathmatch
Mickey Mania
Tekken 2
Tekken 5
Crash Team Racing
Wolfenstein: Enemy Territory
GTA Vice City+San Andreas
Most games made during the last 15 years are so long that there's no sense to beat them more than a few times, even if that. Naturally less linear games offer more replayability than ones where the storyline and all character interaction remains the same no matter how you play the game.