I wish you could specify releases in Darkadia and get proper box art depending on what version of a game you have. I'd love for more frequent updates to that site.
The only other organization tool I've used is VGCollect. They're a little better with box art, especially with unique releases like limited editions. They also support hardware and accessories, if you're into that.
I haven't used either extensively, but they seem comparable. The only major difference I've noticed are that VGCollect also can track your hardware (consoles and accessories) and has a mobile version of their site. Darkadia uses the Giant Bomb API to pull their game data, so that might sway you too.