I understand that the Red is NTSC and Black is PAL, but that was basically just a community decision. I downloaded VERTICAL covers and made modifications for my N64 collection since I have NTSC games and wanted black covers. Usually these were very minor modifications of the PAL versions (simply removing the "PAL VERSION" on the spine and replacing the PAL rating with the ESRB symbol.
Others, like Star Fox 64 required more heavy modification of the NTSC version since the PAL version is Lylat Wars. I did not change the bottoms of the backs (like the warning labels in different languages) since this is very minor issue to me. I was doing it just for my collection, but if there is a demand I will happily upload and share. These are the ones I did:
Super Mario 64
Mario Kart 64
GoldenEye 007
LoZ: Ocarina - kept PAL art/spine
LoZ: Majora - kept PAL art/spine
Diddy Kong Racing
Super Smash Bros. - changed front picture from PAL to NTSC
Donkey Kong 64
Star Fox 64 - my first and arguably most painful attempt. Noob to photoshop didn't help.
Perfect Dark
Banjo-Kazooie
Banjo-Tooie
1080 Snowboarding
Turok
Conker's Bad Fur Day
Bomberman 64
Paper Mario
Keep in mind, this was my very first usage of Photoshop and I was shooting for a "very good" and definitely not a perfect.
This is all well off-topic. Where do I report errors for covers? I noticed that I think the two Banjo-Kazooie games and Conker didn't match the other covers. (most PAL vertical covers have the "64" at the front and spine as red, these were still white on the front).