The entire sequence onboard the LP-9999. Zone of the Enders inspired combat! Plus, the cutscene following victory ends with Wayne killing the Big Bad.
Lost Planet 2
Red Eye in 3-3. After spending the last two chapters of the episode running like hell, you catch up with an enemy railway gun and steal it. Before you can enjoy the victory, you get attacked by the same Cat-G that smashed your first train. So you decide to use the gun on it. The fight has you scrambling around the gun, loading shells, fighting off akrid swarms, and repairing the gun in between shots.
Near the climax of the game, the Ex-NEVEC Commander sends out a message to everyone on the planet, asking them to help stop NEVEC's latest destructive plot. It's a fairly Rousing Speech, and at the time you hear it, you're navigating an orbital minefield in a VS on your way back down to the planet's surface. Awesome.
The whole Rig vs. Rig battle against Laroche near the end of the game. A true Final Exam Boss that requires you to use all the Rig techniques that you have learned throughout the game, plus a chance to give a real beatdown to the annoying French Jerk who's been making fun of you since the beginning.
The final battle against Isenberg, Peyton converts his rig into a drilling platform in the heart of Nushi and then battles against Isenberg's armed-to-the-teeth rig on foot and wins, then after a struggle Peyton manages to kill Isenberg by sending him into the drill
Isenberg is actually using a Vital Suit, not a Rig, which makes this even more impressive as his mech is a dedicated war machine. Jim's solution to this is to sic the Akrid on him: there's just something awesome about making the Akrid fight him.