I recently started to wonder about FTL mods. I wasn't able to find many, and honestly didn't try very hard either.
Luckily the Steam news feed brought the information straight to me! PC Gamer website has an article about what look like fun re-skin mods for the Kestrel and Engi ship, with references to more mod sources at the official forums.
I should see about getting some of this into the wiki somewhere.
Also, FTL is 40% off right now on Steam.