In terms of original games (no remake or third version) I'd say Black 2 and White 2. While I haven't finished it yet, I can appreciate the improvements on BW, and the post game is very extensive.
Third versions: Platinum is the best, hands down. It renders Diamond and Pearl completely obsolete.
Including remakes: HeartGold and SoulSilver, to me, are the best Pokémon games period. Gen 4 graphics, music and mechanics but with Gen 2 story and setting.
Overall HG/SS > Platinum > Black 2 White 2 > Emerald >> all