Boot Liner
At one point I had a bit of a leak in the boot and after some thorough investigation I found that water was entering from behind my drivers side rear light. The problem was a loose bolt which meant that the light lens wasn't behind held close enough to the car. So I pushed the lens in close and tightened the bolt and that seemed to rectify that problem.
Next, after speaking to two members on a forum I found that other leaks are sometimes caused by the bolt that holds in the spare wheel. So I emptied all of my bits out of the boot and stripped out all of the carpet and dried everything inside. Then I left the lid open for a few hours to dry properly and get some air in.
Once everything was out of the boot I moved the plate pictured below and the bolt in it and found there was some water congregating around it. So I tightened it up properly and then spread some silicone sealant around the plate and bolt hole to stop water splashing up from underneath the car. I also used some waterproof Gaffer Tape™ to seal in the edges of the boot and keep all of the electrical cables dry.
I also bought a waterproof boot liner to put in the boot, so it could be easily wiper down if anything was spilled. I put my carpet back underneath for soundproofing and then put the lining on top.