- The Earth Alliance ships from Babylon 5. Absolutely no sense of style; they look like unfinished Erector Set projects.
- The Daedalus-class starship from Trek. I *hate* that globular primary hull.
- Serenity from FF.
To be fair, I don't think the Earth Alliance or Firefly-class ships are in any way meant to look good. The former are meant to look as realistic as possible (spinning segments for artificial gravity), and the latter is meant to look like an ugly, over-used working-class freighter -- the outer space equivalent of a pickup truck. And, personally, I love both of them for it.
The Eagles from Space:1999 are designed realistically and are meant to be workhorse space vehicles, but in my mind the Eagles are beautiful compared to those ships from B5 and Firefly. A good designer can work within those guidelines ("realistic" and "over-used working-class freighter") and still come up with something aesthetically pleasing.
Ugliest Trek ships? Of the hero ships, no doubt the Excelsior-, Galaxy-, and Sovereign-classes are butt-ugly (with apologies to ugly butts everywhere).