for dc games, whats wrong with the original cases?
most games in case should be available for dirt cheap.
japanese games just used normal cd cases, which can be had for cheap nowadays
For me, personally, it's an issue of space management issues and aesthetics.
I have my entire collection of console games (minus some CIB stuff I keep separately) kept on a bookshelf with adjustable shelves. Everything is easily accessible and properly organized. I could adjust the shelves to have all of my CD cases fit snugly in their own little section (and for a while, that's what I did). But what happens is that I end up with unusable space due to the height difference between UGC/DVDs and the CDs, and the fact that I don't have enough CD-cased games to fill up another shelf. One way of dealing with that is to have the CD shelf use the same height measurement as the other shelves, but the void of unused space above the CDs looks crappy.
So I case 'em all up in DVD cases with covers now. Also, while a single DVD case is wider than a CD case, I have a number of multi-disc games that end up taking up less space now due to using multi-disc slim DVD cases. So I've actually SAVED shelf space in the process, plus I'm able to keep the manuals with the games in the DVD cases and preserve the original CD cases in storage so they don't get scratched up anymore.
But really, this all boils down to personal preference.