woah ancient thread, but for posterity, My 1995 E320 Wagon was having the same problem. At first I noticed mild dampness. It perplexed me as I couldn't fine the source. Then one day after a particular heavy rain storm I went back there and it was literally flooded. That was it. I was going to find the source. By total accident I pressed my hand on the rear window and to my shock, it almost fell out. After resetting the rear window gasket my car is dry as a bone. In retrospect, I had been moving a lot of boxes and most likely overfilled the back "trunk" area and upon closing the hatch, something must have pressed the window out. At first ever so slightly, just enough to cause dampness. But it loosened over time and essentially detached itself. Luckily I caught it at home, and didn't have the window fly off on the highway or something.

Just to close my own post a few years late
 

well my leakage problem is finally gone after replacing the tailgate seal. The hard to diagnose condition was due to the fact that the seal was leaking from the backside by the latch. by the backside I mean the actual side that is typically glued into the channel not the front facing surface that makes contact between the tailgate and the seal mounted to the body. As with most wagons and SUV's the airflow dynamics are as such that wind and water is drawn back towards the tail end of the car in a vortex. In my case the water was litterally drawn up past the backside of the seal (between the seal and the mounting channel) and up into the footwell.

After installing a new tailgate seal and properly gluing it to the channel the problem has gone away.

Hope that helps others
Cheers :D

Sun roof tubes should flood mid section of car but remove the rubber drains from there and see if they are clogged with dirt, with them out also pour water on both sides of sunroof to make any other dirt go through with the plug out. I got 6 inches of water in my footwells when we had a bad storm last year that was a culprit.

I have also heard some other wagon owners that the antenna seal and rear hatch seal can allow water further back. I hope this helps.

My 300TE had water come in around the shocks that held up the tailgate, I think the rubber around the roof rack had gone bad. Had the same issue w/ W210 wagon, used black RTV to carefully 'reseal' the rack and haven't had any more leaks, knock on wood...