Fixing Boot and Trunk Leaks with Leaky Seals and SunroofsA guide to fixing boot and trunk leaks when leaky seals and sunroofs let water get inside and fill up the wheel well causing rust and mould.

This guide was written based on my 1996 Honda Civic Coupe; however, the principles should be the same for all car boots/trunks.
I have had a boot leak for the past few months, and it's been driving me up the wall as I can't seem to find all the places it's leaking from. So far, I have found four separate areas where water can (and has) entered the boot area. I have plugged all the holes now, and this information should help everyone else find where the boot is leaking from.
First (and most obvious) is the sunroof drain hose. Clear plastic tubes run down each side and slot into rubber linkages, allowing water to drain outside the car. There is one on each side of the car, and one of mine was unclipped, draining rainwater into the boot.
Second is the rubber boot seal itself. Mine was loose and not sealing properly, so I sealed it with silicone sealant. Sometimes, the seals get deformed, and you can "massage" them back into shape or stuff some foam padding on the underside to help them keep shape. You may need a new one if the seal is torn or physically damaged.
Thirdly, does your bumper look like this:
If so, it may be because the clip holding the bumper on may be broken, and you may leak it as it isn't sealing properly. I just popped the bumper back on the clip and covered the whole thing in sealant (and hope for the best!)
Water was getting in through a leaky joint near the filler cap. Again, I filled it with sealant and will hope for the best. The final pic shows the inside of the filler cap and the wheel arch.
This one was messy, but I will clean it up later.
I used Unibond roof and gutter sealant, though any silicone should be OK. Hope this helps everyone who leaks. If I find anything more, I will update this page.