This troper would argue that the ending, in which Jack escapes Varrigan in the midst of his victory celebration, all while Ox's "Soul" plays. The track is about repenting for one's sins despite having done horrible things and trying to find more in life, (presumably) Jack's thoughts, now free from the games forever. The announcers' credits commentary is awesome, too.
The final boss should get a mention. Not only is it Jack's most evenly matched opponent, but the fight is against none other than the Black Baron, AKA the guy who gets mangled in each level by his own girlfriend. Suddenly he gets serious and shows exactly how tough a guy who keeps coming back from death can be. The kicker is his taunt to Jack right before the fight.