My car sits outside most of the time, and lately I had some coats in my trunk for a couple days, it rained about 4in and I went to take the coats out a couple days later and they were damp and smelled sour. The floor was wet there too... Is this a problem these cars have or is the trunk lid seal leaking or maybe even the rear window seal? The trunk seal looks fine, there are no obvious rips or anything in it.

 

Make sure the trunk seal is pressed down all the way and that it's not folded in any spots. I had been working on stuff in my trunk and thought I had put the seal on all the way but realized it was not pressed down all the way in one spot when I noticed water had been getting in.

Be sure to check the seal around the top of the trunk. Won't hurt to pull it off and put it back on just to be sure. I don't believe this is anywhere near a common issue.

 

I've read this issue with other 5th gens before and the tail lights are always brought up.

Fix would be to put more butyl tape on.
Take off the tails to do so.

 

The wet spot on the trunk floor is too far forward to be a taillight issue. I'll have to pull that seal off and reinstall it, to see if that helps.

 

It's probably not the seal. The seal is more for blocking air than water. Especially in a light rain. The water is channeled around the seal and to the ground. You wont gain anything by pulling the seal and you might damage it.

Pull the interior panels out of the trunk and look for a "riverbed". If you can't find the leak that way, crawl into the trunk and have someone spray water over the roof and rear glass. With a flashlight you should be able to find the leak. If you don't want to find it first you could just move to the fix since it's cheap and easy.

I recently fixed a few leaks on my wifes 2000. It seems like Nissan used some type of body filler in the seams that's breaking down now. I found leaks in the circled areas in the photo. I just pulled the photo off the web so don't ask about the speaker.

The channels between the rear window and the lights has an overlap that was letting water through. To fix it:
*Clean it really well. Especially if the car lives outside. Use a stiff brush to get as deep as you can. You might want to pick out some of the old fill depending on how it looks.
*Dry it inside and out with a heat gun or hair dryer.
*Run some waterproof silicone caulk (comes in different colors or clear) over the joints and force it into the cracks with your thumb. You want to force in as much as you can rather than cover the outer surface. Keep it smooth, you don't want to create a dam to disrupt the flow of water. I used JB Weld but caulk will work as well. It'll be easier and comes in colors.

I thought the leaks near the tails was the seal but replacing it didn't stop the leak. It turns out there was another Joint right by the tail that was letting water past the body fill. I used a similar technique as above and I did use caulk on it.

If the tail light seal is leaking they make a gooey strip to replace it with. You can get it at the auto parts store. The seals are pretty good though so they shouldn't be leaking.

You'll have to pull the seal just around where you're working but don't remove the whole thing.

I did this last year and her trunk has stayed bone dry even through some big storms.