I've only recently started collecting SNES games, and I've noticed (mostly by the number of downloads) that retail style covers seem to be preferred over custom covers by around a 2:1 margin. Maybe it's the Genesis collector in me, but I like the custom covers better because as you're looking at it from the front, it's oriented the right way (like a Genesis clamshell). Same with N64 - I have just a few, but I've printed the customs.
When it comes to Genesis however, I will always use the retail artwork (unless a custom is all that's available). Of course, it's really a moot point as far as orientation because all Genesis covers sit the same way in the clamshells.
I'd like to hear from other SNES collectors as to what they prefer and why. Maybe as my collection grows my tastes will change. If I acquire some complete in box SNES games, I may want to switch to horizontal retail style covers for similarity - but for now I have just one CIB game (Gradius III).
Also - does anyone know if there's a custom cover for SNES-Art of Fighting anywhere on the site? I see that there's a "New SNES Covers" thread in the forums, but it's nearly 200 pages long. If anyone knows of one, I'd greatly appreciate it.