Rainbow Dash
It's a My Little Pony! Which I believe is something from Breaking Bad? (I'm sorry, I'll stop that now)
ResoNyan
It's Nyan Cat! Personally, I think Housemarque should have programmed it so that any ship with 'Nyan' in the name leaves a rainbow in its wake. That's what I would have done. Still, there's always space on the hard drive for another patch...
Gomez
Too cute. And I don't care about all the trash-talking--I still want Fez 2.
Human's Revenge
There are a lot of Human-shaped ships, but this one looks cute and is carrying a massive gun to get his revenge on the enemy threat that's turned him red so very many times.
3D 8bit Mario
There are a LOT of Mario sprites in the list, but very few have been given a true 3D treatment. This one has the right colours, the right profile but crucially a believable depth too. Great job.
Galaga
Shout it! Galaga-laga-laga-laga...
Iron Man
Is this the legendary Iron Giant? Or even the Tony Stark-in-a-suit superhero? No, it's a man in his pants, doing the ironing. Brilliant. This one wins many internets.
Lincolnator
The Lincolnator is Abraham Lincoln. If anyone can save the last humans, it's honest Abe, right?
Gummi Ship
Ah, now that's clever. You see, the Gummi Ship in Kingdom Hearts can itself be designed by the player! However, this is the default, non-player-designed creation. The irony will probably make this one implode any minute, so grab it quick.
paper plane
It's a paper plane.