Hello everyone, new to the forum, and new to the game, I just got it last week.
First of all, awesome game, it's super fun.
Second, thanks to DarkFrost for his FTLEdit ship editor, and thanks to alextfish for his guide "Creating Player Ships with FTLEdit"
Without further ado, I present to you my 2nd custom-made ship for the game (the first was just a test to learn how to do it)

The Cobra Class Destroyer is a ship from the Warhammer 40k Universe. It is known as the smallest independent Imperial ship (ie it can patrol alone, and is not a fighter or bomber based on another ship).
More info: http://wh40k.lexicanum.com/wiki/Cobra_Destroyer
Due to difficulty in finding an overhead image of the ship of suitable quality, I decided to try something different and make the ship from a side view. Sure, the crew and rooms are all top view, but I actually think it looks pretty good.
The Cobra is armed with a dorsal weapons battery (a Burst Laser Mk II in the game) and prow-mounted torpedoes (2 Hull Missiles in the game). Note that the crew are not to-scale with the ship, as the ship is approximately 1.5km long (yeah, 40k ships are big). I like to think that instead of individual characters, each crew member represents a team of people, so the pilot is not just one pilot, it is the entire command staff on the bridge of the ship, and the weapons guy is not one guy, it is a large number of gun crew, the ratings that load the weapons, the engineers that serve them, etc.
The ship is fully functional in the game, with working rooms, weapon mounts, shield image, cloaked image, ship list icon, etc. The only reason why I do not consider it 100% done is that the base image still needs work (I need to remove those white spots left over from when I removed the background), and it needs to be balanced properly. The balancing, however, is not an urgent issue for me, since the eventual goal is to replace all the ships in the game with Warhammer 40k/Battlefleet Gothic ships, so balance will need to be dealt with later. I suppose the extra-long-term-way-beyond-my-ability goals are to completely overhaul the game, replacing everything with new 40k-based events and text, maybe replacing the room images with side-view 40k ship interiors, replacing the crew sprites (yeah, insanely hard)
Here are more pics:
The ship list icon:

The ship base image in the hangar:

The ship rooms seen in the hangar:

The ship with all room upgrades:

The ship with cloaking activated:

and finally, the download. It is GMM compatible, and it replaces the Rock Cruiser A in the game. Just drop it in the mods folder, activate with GMM, and you're good to go. Go purge the stars in the name of the Emperor!
https://www.dropbox.com/s/9j5o6cq8sxm6x ... word.ftl?m