There are so many to choose from, my brain hurts just trying to pick.
Pretty much all the ships that appeared in the series are excellent, but the Omega, G'Quan, Sharlin and Vorlon heavy cruiser are probably the most original and beautiful.
The Shadow ship was perfect for scary nasty menace, but getting them to look scary on the table is more difficult.
Of the original ships for the game personal favorites include;
Var'Nic
Bin'Tak & Ka'Bin'Tak - they are very similar after all.
Liati - Personally got no problem with the phallic nature of the ship, see the quote in Excession about phallic ships f***ing planets.
Octurion - looks like what it is, a massive flying fortress.
Also some fleets just have a consistent feel to them that is particularly good;
Dilgar fleet - cohesive design throughout, and when painted well they look elegent and menacing at the same time.
Gaim fleet - again cohesive fleet style, un-symetric ships and just a very alien feel to the fleet.
Crusade EA - only earth fleet that actually looks at all good.
Oh, I've probably missed an aweful lot of good ships out, but that's a good thing. Over 50% of the ships for ACTA look GOOD, and of the rest, half of them are more than acceptable. I should know, I've put virtually all of them together and painted them over the last couple of years.