I never played JC1 and it seems to be not as interesting, so..
I think in JC3 it has to be Falco Maxime with FOW on. I mean, a homing nuke, come on! If we don't consider FOW, then maybe I'll go with Cava Montana or Vulture. If we count only expansion packs, the Stern Section and Bow Section (eDEN Airship) might be up there, also Novola Central Detention Camp.
In JC2, it's gotta be Wajah Ramah Fortress.