If we're talking pure design - Courier, Cobra, FAS in ED.
In gaming in general...tough question. Considering that space genre only resurrected recently most of the memories are recent, and I can't really remember playing many space games in the older days.
Reapers from ME were absolutely fantastic. Menacing, intimidating. And their voices...Oh, gave me chills.
Some of the ship designs in Space Rangers were interesting, even though this game was trying to be Elite with top down view and turn-based movement. I still love SR 1 and 2 though. Highly recommended, even though they're pretty old games.
Also, any ship I've made in Space Engineers when I was into that game

The fact that you could have anything you want, and it would work(sometimes) meant everything to me. Now when I think of it...I have to go back to that game. So much new stuff was added.