All of Episode 44; especially seeing as Richard was losing sleep to get it out as soon as possible
Not to mention Wario's fight with the Darkness.
Let's just say all of Act II Part 3 is a Crowning Moment of Awesome
Let's not forget Luigi's creative solution in Episode 22, Part 3.
Snake and Liquid's final fight to the death on the railroad tracks.
Snake and Liquid's SECOND final fight.
In Episode 59, Shadow Mario's back, baby!
Snake kills the back from the dead Tommy Vercetti.
Snake: I'm sick and tired of people coming back from the dead for no reason. This time I'm going to kill you and you're going to stay that way.
Tommy: Oh, I don't think so.
(Snake opens fire)
Waluigi Vs. Blaire Vherestorm: After taking out Snake and the pirates, Blaire turns his attention to Waluigi. Waluigi warns him that he's going to make this brief. Then he unleashes the Mega-Fireball. He also stabs him dead with his lightsaber. Considering this is probably the first major victory for the heroes in the War, this was pretty awesome.
The battle against the Pirates and the Ninja in the finale, with a healthy dose of funny moments sprinkled in.