Having experimented with several different methods, uniformity, retail, etc. I have come to the conclusion that (for me) uniformity of some kind is ideal. For NES, they need that black NES logo square up top. For N64 and SNES the spines need to be the same. The fronts, backs etc don't matter so much to me, but the spine is by far the most important thing.
I suggest trying some stuff, seeing how it looks and going from there. You never know what you'll find. For example, one thing I learned that I absolutely won't compromise on is that all my genesis titles need to be uniform red stripe. I just hated how they looked mixed with black, green, etc.
So I say play around, print one or two of various covers, and see how they look.