My opinion is colored by playing Star Trek games besides just watching the series.
Federation - I like the look of the Intrepid-type. It is a nice departure from your traditional Federation design while still maintaining the look of a Federation ship. Game experience has taught me that Defiant-type and Sovereign-type ships are probably the best.
Klingon - It is hard to argue with the Negh'var. Big targets though, like Galaxy-type.
Romulan - D'deridex-type hands down. Raptors are cool but the shield inversion beam is cooler.
Borg - Cubes are cool but the Diamonds are probably my favorite.
Cardassian and Dominion ships show a complete lack of imagination and while they look tough...well looks are at least partially deceiving.
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