The USS SuperAwesome
I mean, the new Type 45 Detroyers, HMS Daring and HMS Dauntless have proper naval names as do the submarines Trafalgar, Ambush, Audacious. The new carriers being built - the Queen Elizabeth and the Prince of Wales - take us a little too far in the American direction, (even if there have been seven previous ships names Prince of Wales) and they’re not quite as good as previous carriers such as Implacabale, Indefatigable, Furious, Colossus, Vengeance and, perhaps best of all, Vindictive.
Yglesias points to Star Trek's starships for examples of good ship names. I think we should go even further. If you're hunting for some ship names that will really make Al Qaeda respect our authoritah, look no further than the Galactic Empire. Well-known Joe Lieberman lookalike Emperor Palpatine had an Accuser, an Agonizer, and (according to the "extended" Star Wars universe) an Eviscerator. Now these are some ship names.
(Yglesias also says "Basically no starships seem to be named after committee chairman or undistinguished former presidents." But presumably, in the enlightened future society that is the Federation, starship-building is removed from the realm of earmarks and appropriations bills and fully and fairly competed. Political patronage is less important to the process, and I'm almost certain that Star Trek contractors that are asked to extend starships by 12 feet don't end up making modifications that ruin the ships' structural integrity and make them unusable.)
UPDATE: The Economist has pwnd me with some truly awesome ship names. USS Batman, anyone?