I thought about this, and it dismays me to realise that I can't think of a single EU ship that stands out to me.
That probably has to do with the fact that the actual technology in Star Wars is basically ignored unless it's a superweapon. EU ships essentially serve no role beyond acting as a backdrop for plot progression. Sad, really. That's one of the things I like about the Halo universe; the various ships and vehicles the characters utilize tend to be fleshed out to the point that they serve as more than just a means to an end.
I'd like to see a star wars story that focuses exclusively on military personnell such as pilots ans bridge crew. The Rogue Squadron novels came close, but Stackpole sucks at writing characters that aren't Gary Stu's.