This is a cool idea. I'd just go with some of the popular skins to start with. Chuck's, Liquid Smoke's (LSX Void), and some other popular ones. Just looking over the popular ones at Mobile-Effects.com, I'd suggest the Alpine skins, the iDrive skin, Brushed Metal and Brushed Aluminum, Bongo.
I kind of like Guino's idea of having separate installers for each skin. Some of the skins get so involved with incorporated extra software, that having it's own dedicated installer might be the best way to go, to keep down the file sizes, and still include everything a noobie user would want to implement. Heavily modded config files, menus etc almost make a separate installer necessary. Otherwise you'd have a custom menu from an old skin showing up in a newly installed skin. (You know what I mean)
The basic skins that don't really have extra apps could be worked into a generic skin installer.
I really like this concept and think it would really set off Road Runner. I'd like to see something in the skin installer that would let the user download and install their car-specific flash logo/clock as well. New users have problems trying to figure out how to implement this. Possibly have the installer detect if the user has the necessary files needed to run the skin correctly (flash). If not, offer to update them.
Webmaster, I saw you submitted your new apps as downloads at mobile-effects.com I'm waiting to add them to the new site rebuild that should be done soon - just didn't want you to think I was ignoring your submission