Christ, am I gonna get it for this…
The USS Enterprise, and all Federation capital ships seen so far. If the Klingons or the Borg had enough sense to target those narrow bits that connect the saucer section to the back section, or the back section to the nacelles, then they could break the ship into four pieces faster than Geordi could say “Hull breach, decks 5 through 7, Captain.”
As SPOOFE pointed out, the Nebulon-B from Star Wars has the same problem. Big front and back sections, connected with a long, thin tube. What engineering genius designed that one? Most Star Wars ships are OK, however.
In terms of sheer uglyness, the Rebel command ship from Return of the Jedi takes the cake. You know the one: the big elongated ship covered with little lumps. It looks like they chrome-plated a turd.