Vaporeon, as Water is my favorite type and he's generally the strongest to use. Leafeon is second, I guess. I did an all-Eevee game in Pokemon Platinum, sans Umbreon since he's a bit weaker at actually attacking. Flareon's pretty good ingame, since you can just give him Return or something and go crazy with his really high Attack. Plus he's got some pretty respectable Sp. Def, so he can take a few special Water attacks before folding.
Also, imho Espeon should get Aura Sphere. It'd make Espeon into a pretty good special sweeper. Ghost/Fighting, IIRC, is absolute type coverage (i.e. hits every single Pokemon, or at least every single mono-type for at least neutral) and it has a good stat spread for a special sweeper. That said, it seems that Game Freak kind of hate the non-Jolteon and Vaporeon Eevees.