I keep mine happily stacked in alphabetical order. The only exception is that if I've been switching between games a lot, I usually keep those toward the top so I don't have to mess up my pile (for example,
Rune Factory 4 has spent a lot of time sitting on top of
Animal Crossing New Leaf lately). I really wish I kept track of the whereabouts of my DS game cases, so I could do the same with them, but I haven't the slightest clue where most of them went. =(
I also became a 3DS Ambassador around this time of year last year--well, technically, I've always been one, but I couldn't get the certificate until last year. So, I've downloaded a few games since then, but only, like, three so far. Pacing myself slowly, I guess.