I second the trading card holder idea. This has been the best solution I have seen people do. DS cases are nice but once you get to about a 100 games this seems insanely space consuming (just imagine adding this to your already existing DS collection). I recently focused and sold most of my games due to taking up too much space. It becomes a pain. Plus, it can get expensive. So, I go cart only on most things. I even do this on Genesis when boxes are fairly easy to find and cheap. I just don't want to deal with it anymore.
I'm ok with Jewel cases and DVD cases.
Ultimately, it comes down to taste.