Ooh I like this topic. There are some really good ones out there, most of there best cover art are from niche games that everyone forgets about. I'll see what I can find in my library of games and I'll post them below:
NOTE: Right Click and choose "View Image" to see full size.
Panzer Dragoon (Japan Cover) - Sega Saturn
Monster World IV (Japan Cover) Genesis
ICO (Japan Cover) - PS2
GunLord - NeoGeo/Dreamcast
Alisia Dragoon - Sega Genesis
Snatcher - Sega CD
Star Fox (Japanese) - SNES
Doom - PC
If I think of more I'll post them later.