Paddy, I can't help but wonder why you consider Alomomola such a bad name. It's just a slight scrambling of molamola, the species of fish it's based on. I admit that Amolomola might have been better, to mix in 'amour' to drive the heart shape home, but then it might have been too heavily associated with Luvdisc (well, moreso than it already is). Normally I don't like attribute + species names, but when you're based on a molamola you can get away with it.
Anyway, my favorite....there are a lot of really good ones, but if I had to pick one out it would be either Carracosta (which I believe is a really creative way of combining 'carrapace' and a corruption of 'coast'; could be wrong, but it still gets the idea across) or Druddigon (have said this before, it sounds gritty and tough and generally fits the pokemon very well).
Least favorite has got to be Golurk for me, though Throh and Sawk deserve mention. It's not a bad name overall, but it just doesn't come anywhere close to capturing the essence of an ancient flying robot golem. I might be biased here because it's my favorite pokemon design in all 600+ pokemon, so it getting a name that doesn't suit it means more to me than any other pokemon getting a name that doesn't suit it, but my point stands. I tend to care more about a name suiting a pokemon than a name sounding cool, and Golurk just doesn't suit it.