As far as the box art template, I'd say the N64. I also like the Jaguar, 32X, and Saturn templates. OG Xbox as well.
Favorite cover art? There's so many good ones I couldn't think of them all off the top of my head. Body Harvest, Top Gear Overdrive, Banjo Kazooie, Killer Instinct Gold, Dark Rift, XG2.
As far as other consoles... Nights Into Dreams, Croc, Ghen War, Machine Head, Shadow Master, Sentinel Returns, Jumping Flash, Kinsley's Adventure, Jet Grind Radio, Rippin Riders, Super Bomberman 2, Hyperzone, Sonic 1, Alisia Dragoon, Kolibri, CastleQuest, 8 Eyes, Snake Rattle & Roll, Cobra Triangle. I think I could go on and on, with cover arts that I like. A lot of times it's not necessarily the obvious titles that have the best art, it's just random ones. NES had so much great box artwork, with all the hand drawn stuff.
Maybe one day I'll take the time to actually make a top 10 or 20 list of favorite cover arts.