FTL has had some awesome new ships created by the modding community, but on the Master Mod LIst there are hundereds of ship mods including mods that have multiple ships under one link. It's really hard to find exceptional ship mods without spending many hours trying not-so-good ships. Fortunately, some of us have already spent those hours. I'd like to get some discussion (or at least a big list) on our favorite ships and recommendations for the best ships, especially now with the upcoming Advanced Edition set to shake everything up.
EDIT 3/2/2014: Well, almost three months later I've decided that even if basically no-one replied, I can still give this list visibility by putting a link to it in my signature. I put the pictures in and I might edit it a little bit more. Feel free everyone to reply and bump this up to the front page again anytime.
Descent into Darkness: Athena
Universally regarded as the singular best ship mod for FTL, it's my opinion that this should be the first modded ship everyone tries. The mod makes many graphical changes, but they're all in service to the Athena. The Athena doesn't start with any crew or starting gear at all. Instead, you get to pick your starting equipment, hire some crew, and other choices. There are 72 possible starting combinations, so make your choices and bring justice, (or your personal revenge,) onto to the Rebels. Includes (your choice between) two of the most fun semi-OP weapons: The Ultrasonic Cannon, which shoots a projectile so fast it's invisible to the naked eye, and the Heavy Beam, a modified Glave Beam that does less direct damage but shreds through hulls on systemless rooms.
*Updated for AE*
There are many ship mods that try and make the Rebel Flagship a player ship. I've seen all of them, and they're universally terrible with one exception: This one. The Imposter will let you kill the Rebel Flagship with a Federation Flagship, and it's everything you could ask for. Polished, balanced, fun, looks great, etc. Please stop making Rebel Flagships with 100 ship tiles and super-overpowered weapons, it's been done to death many times over by now.
*Updated for AE*
The Potential starts with 60 power bars, enough to instantly power absolutely everything you buy. In exchange, you start with an extremely bare-bones ship. You have the potential for an extremely powerful ship, but until you get there it's a challenging ship that mixes up normal ship progression.
*Updated for AE*
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BIOLOGICAL UNITS UNNECESSARY
I've seen many no-crew automated player ships, and in my opinion this is the best. I say that mainly because of the far too sensible inclusion of the slug-gel augment, and the absolute impossibility of getting crew. The only thing worse than having your drone system breached and wrecked is buying a medbay and a crewmember to run back and forth to fix it. (An auto-ship's auto-repair doesn't work if a room is breached.) In this ship, you can't get crew and you don't want crew; you blow crap up and doesn't afraid of anything.
The Black Opal
Ghosts are a cut 8th crew type that can be used through mods. (I believe that they were originally intended to be the crew of auto-ships, but I might be wrong there.) Ghosts don't suffer suffocation damage, but only have 50 hp. This is a boarding ship. You have a beam that causes breaches (and nothing else) and an ion to get through shields. It sounds very difficult to start with, and it is... unless you're facing automated ships. Your ghost crew can board the airless rooms, and your beam can disable the auto-repair in whatever rooms you choose. Find any damage-dealing weapon and you can also destroy the auto-ships, too. A rewarding ship for those who have mastered advanced boarding tactics.
One of Crusher's Type C(hallenge) Ships, this extremely challenging ship starts with 4 Zoltans and zero ship power. It's 'fun' to completely rely on shuffling your crew around to power stuff, and you'd be surprised how much needing to buy those first power bars can put you behind the usual upgrade advancement. The weapon it comes with, the Phase Beam, is also rather quirky. It pierces 2 shields, but it's only a 1 damage minibeam that takes 20 seconds to charge. It feels more useful than powerful.
First off, this ship has the rather unfortunate bad luck to not be mentioned in the OP of the thread for the modfile it's included in. Anyways, The Liquidator is a ship that starts with no weapons, drones, or teleporter. What it does have is a dummy augment that sell for 200 scrap at a store. Instead of choosing what kind of loadout you want to tackle the game with, with the Liquidator you hightail it to the nearest store and see what the RNG will give you. It's highly luck based, but sometimes it's fun to have a really weird loadout, especially if you're using a mod that puts extra weapons in the game. And I think the layout with the cross in the center is fun, even if it might be a tiny bit bugged. Unfortunately this ship has some interface problems that show up after purchasing its systems, probably due to it including too many weapons and drone slots.
Mantis Thin Mint
I like this one because of its seriously delicious looking hull, and its crazy loadout. Mostly the minty hull though. It's a ship with both stealth and a pre-igniter, but it starts with no shields, only 2 weapon slots, and terribly pathetic weapons... none of which have been any serious obstacle to me completely wrecking all my enemies with that pre-igniter. Really, looking back at this list, while they've all been favorites the legitimacy of them being 'best' fades as you go down the list, so take this one as just a ship I like a bunch if you have to.