The very first time I saw a puddle of water on my front passenger side floorboard, I thought one of my idiot friends spilled a bottle of water and declined to inform me of their stupidity. Then, a few days later after I dried the puddle I noticed it reappeared. I didn't carry any passengers during that time period, either. Uh oh, looks like I had a serious problem in my hands. A puddle almost formed in my crotch.
Then I heard about a drain mounted on the firewall inside the engine bay that often gets clogged, which causes water to back in the A/C recirculation doors.
It's located on the passenger side of the engine (US cars) and is roughly level with the exhaust manifold. It is pointed groundward with a flat outlet end to prevent debris from entering, but it also prevents crap which got in there from leaving. (Some say the exhaust manifold heat may seal it up as well.) I pulled the rubber drain out and stuck my finger in it. Sure enough, there was a ridiculous amount of dirt and crud in there. I cut off the end so it was freer flowing and hosed it out, then spent half an hour trying to reattach the sucker back on the firewall.
I took out the passenger seat by removing the four bolts that hold it onto the floorboard, then removed the passenger side kick panel in order to peel back the carpeting and find the water source. When I pulled the carpeting back, I was astonished to find not a puddle of water, but a good sized lake two inches deep! It was so deep battleships could've floated around there. After scooping all the water out, the only thing I could find was a white drain plug located towards the firewall. I opened it and felt some dirt in there. I scooped it all out with my fingers, dried the carpet, and crossed my fingers that it did the trick.
The next day it rained and I had another aquarium on the passenger floor. Someone suggested that I had a clogged windshield drain, which was causing water to come up through the recirculation doors in the A/C housing and runs towards the rear of the car because the rear is lower. Makes sense. I pryed off the right windshield grille with a flathead screwdriver and it looked clean as a whistle. I even got an air hose and blew it down there, but nothing happened. Scratch that one off the list.
Problem solved! Or was it? About two weeks later I drove through a heavy rainstorm feeling completely confident that my water troubles were solved. I glance down at the passenger side carpet, and you guessed it, there was a dark puddle staring right back at me. Doh! When it stopped raining, I decided to open the sunroof and test out the drains. I poured some water on the front driver side drain and it came out a hole just under the driver's side door. Then I did the same for the passenger side, but nothing came out. I poured some more in, still nothing. I looked under the car and discovered a thick pile of mud/dirt collected around the drain. I loosed everything up with a flathead screwdriver, and out came all the water! I did this last winter and the problem has never come back.
I suppose Occam's Razor probably comes in handy here. So if you have water troubles, try checking that sunroof drain first. :)