Crack in the seam sealer, lack of butyl under a piece of trim, leak under a door rubber, and sometimes the water will come in one place, run down the roof at a seam or pinchweld and show up a fair distance from where the water is actually coming in. Some leaks can be found by spraying very soapy water on the area you want to test, close the windows and doors and put the heater blower on high. Often you will find bubbling at the leak. Works excellent for leaky windows. You can also go around with a blow gun hooked to a compressor from the inside.
Often if you use compressed air around a suspected leak from the outside, you will see water coming out from under a crack in the seam etc. This might point to your leak as well. I have had to spend a fair bit of time finding possible leaks, then taping over them, running water again, taping over another spot etc etc
It is all much easier if you pull the headliner, but it's up to you. I guess it depends on how badly you want to find and fix your leak dude.
