It's tough to say. Just going by the boxes themselves and less about art, I love Sega Genesis and Master System plastic boxes, cause those are durable as hell.
I also love the big glass CD cases, so Saturn and Sega CD. They are big, they have a nice inside to them, they really stand out visually I think.
Playstation also with their long boxes for the early days are great, but I feel their quality is lesser to that of Sega's. Look good though.
Nowadays, the best stuff are the limited editon metal tins they have for different systems. Those ones are pretty great, usually have unique cover art. I don't have a lot of these myself, though I have it for PS2 Resident Evil 4, Final Fantasy XII, and Halo 2.