A few years ago when I took off the factory spoiler and filled the holes I sanded the trunk to bare metal and spraypainted it with Rust-Oleum. My roof is also painted with it. Just this regular kind:
http://www.rustoleum.com/CBGProduct.asp?pid=24
It's just one coat, with no clear or anything, and it's been through rain and snow pleny of times since, with no problems. I use it on everything, because I have rust-phobia when it comes to my car.
They also have a 'Professional' 'High Performance' line, with most of the colors:
http://www.rustoleum.com/CBGProduct.asp?pid=95
Recently I found out that the nearby Lowe's carries all of the colors, so I have switched to using the 'High Performance' enamel, which I'm assuming should be even better, although I don't have any complaints about the regular one. I even used it to cover the rust on my rocker panel years ago, and it still hasn't shown through, haha.