I know I'm responding to an old thread, but I just fixed a water ingress problem on my 88 535i (no that model matters) and wanted to share my solution.
My old foam tail light gaskets were hopelessly degraded so I replaced them with 3M Strip Calk (yes, I spelled that right) on a recommendation from mye28. It worked perfectly and sealed up great, even under Hurricane Sandy rain. These come in a pack of 60 short strips that can be stacked and twisted together to form a thicker gasket. It's never supposed to harder or dry out, so it should theoretically last forever. Or at least longer than a set of new OEM gaskets, and it's about a quarter the price. Only $16 shipped from Amazon vs $50 for the OEM gaskets.
My trunk seal was leaking too as evidenced by water running down into the tool tray and dripping off the top of the trunk lid. What I didn't realize was that the original seal was supposed to be one piece. You'd never know from looking at my car - it had two perfect cuts on the upper left and right corners along the diagonals, following the seam. I thought there was one piece along the top and another U shaped piece along the bottom and sides. Nope. It was cut for some reason and as it aged and shrunk a little it was enough to let water run in and along the plastic trunk lid liner. This is actually one time I'd recommend something by the manufacturer Uro (gasp, I know.) but I bought one from AutohausAZ for $41. With a valve cover gasket and some crush washers for the oil spray bar I hit $50 for free shipping. The OEM gasket is $75 by comparison. The Uro one came in a nice sealed bag (important to keep plasticizers from evaporating while in storage at a hot warehouse) and is a nice heavy high quality piece. It installed easily and I used an aerospace grade Dow Corning 3145 RTV to glue down to the body. I applied some Molykote 44 grease as a lubricant to keep it from sticking to the lid. That stuff works great on door seals too and keeps them from sticking. I have access to that stuff, but an Autozone RTV and silicone spray should work in their place. Just make sure to use acetone or a strong solvent to clean up the old glue. This is also a good time to take care of any rust you find under the seal. I was fortunate and mine was a Florida car until recently.
Just a heads up in case anyone else found that their trunks were leaking after all the recent rain. For less than $70 you can get it all sealed up again with new parts.