My favorite line isn't a line at all, rather it's Jack's face when he realizes Cotton doesn't have a tongue--almost the same face when he, Gibbs, and Elisabeth are talking about Beckett and he makes the yuck face.
I also love the line "There's nothing wrong with my compass" then the pull away shot shows him with the appropriately placed cannon giving the line prior a whoooooollllle diff meaning.
And good gawd, when he stares her down, saying nothing and then says "pirate"--damn that was hot and then some.
Tex! How have you been, my dear? Great Jack references, too. The man has a million and one expressions and all of them are great. Along the lines of learning Cotton doesn't have a tongue, I very much like when he hears Anamaria's voice and starts inching his way towards her. You can tell he's dreading it! Lol. And his reward is a slap.