This question comes straight from a conversation that Abby and McGee have in the episode "Road Kill." From the episode:
ABBY: I'd pay to see the right battle. Like Leroy Jethro Gibbs versus...
MCGEE: Ziva!
ABBY: Oh, McGee, I was thinking like Terminator.
MCGEE: Which model? TX? T1000?
ABBY: All of them. Gibbs terminates.
MCGEE: Alright, how about Gibbs versus Godzilla?
ABBY: King of the monsters? Toast.
MCGEE: Mothra?
ABBY: Wingless in a nanosecond. Come on, McGee, give me something fierce. Boss-man's got mad skills.
MCGEE: Alright. Gibbs versus... [Gibbs enters.] Gibbs.
ABBY: Oh, that's good. OK, so evil twin or a clone?
I think this raises the obvious question: who could beat Gibbs in a fight? Goku obviously could due to Goku's Rule (Goku always wins, but everyone else has to try and fail first).
Franks would be an interesting option. So would Director Vance.
Gibbs versus Sephiroth would be fun too, because Sephiroth would at least toy with him for a while, and as Advent Children proves, Sephiroth is unkillable but more than willing to toy around with challengers.
Chuck Norris
Chuck Norris. No doubt.