The best is the scene where Flynn is driving his re-created Recognizer:
Flynn: Pretty good drivin', huh?
-He accidentally slams the vehicle into the ground-
Bit: No.
Flynn: Who asked you?
Squealing tire sounds as the Recognizer barely turns a corner and takes out both sides of the corridor.
Alarms going off as Flynn cuts through a bridge and drops a tank that was traveling across it.
Bit: No no no no no!
Entire scene ultimately ending with the Recognizer destroyed, and Flynn flung head over heels into the program building.
When Flynn recovers after his attempt at reflecting a beam in order to create a junction so the Solar Sailer Simulator could switch beams, he's still a little dizzy, which makes for a few funny lines.
Flynn: Tell the guy with the jackhammer to lay off, will ya?
CLU speaks only in a Machine Monotone, with one exception: He is driving a tank, being persued by Sark's security programs, and realizes he is about to plow into a wall, at which point he Screams Like a Little Girl.