My favourite cover for a game by a long shot, the original Final Fantasy for the NES was both simple yet complex and detailed at the same time, and the stark contrast and coloring make this a true work of art.
Rockstar first started the multi-windowed cover that has become their trademark for the GTA series with GTA3, but it was Vice City, with its bikini girl, neon sign, guns & thugs and boy toys that will be remembered by all. Also, the GTA logo itself is possibly the best one out there.
Dungeon-crawling RPGs usually use sexy female warriors or dragons to sell copies, but Arx manages to blend sexiness, strength, mystery and sorcery into one female character on the cover, and the blood-soaked dagger is an incredibly nice touch too.
BioShock's cover was so stunning in all its steampunk glory that it took me months before I even realized the freaky little girl in the background. Not the mention one of the greatest title logos ever seen in gaming.