When they plan on putting Jessup, Kaffee did a dead on impression of one of Jessup's earlier line. Further funny points because the entire scene was ad-libbed by Cruise.
When Weinberg was introduced to Galloway
Weinberg: I have no responsibilities here whatsoever.
Galloway being flatly told that she should leave so the others can talk about her behind her back.
Kaffee is practicing softball with his team when Lt. Spradling, another naval prosecutor, interrupts to talk to him about one of Kaffee's clients, who's being charged with possession and being under the influence while on duty.
Kaffee: It was oregano, Dave. It was $10 worth of oregano!
Spradling: Yeah, but your client thought it was marijuana.
Kaffee: My client's a moron. That's not against the law.
Later, while Kaffee is practicing softball again, Galloway drops by to wonder why he's practicing softball and not worrying about his clients. Kaffee's response? "We need the practice."
Galloway: That wasn't funny.
Kaffee: It was a little funny.
Later in the same scene:
Galloway: I don't think you're fit to handle the defense.
Kaffee: You don't even know me. Normally, it takes someone hours to discover I'm not fit to handle their defense. (off Joanne's Death Glare) Oh, come on, that was funny.