I have a 1995 wrangler with hard top and full doors.  Everytime it rains the jeep leaks like crazy.  It's not comming in around the hardtop, or doors.  And I replaced the windshield seal so I don't think that is the problem.  I have tried to find the leak with a buddy and a waterhose but still can't.  It is a daily driver so I don't really want to pull all the carpet out and say heck with it yet. 

Any Ideas?

with my '97 it was the air duct under the glove box.

check the drain tube ... i could be blocked.

on my jeep, the air duct was cracked.

Pete