I recently bought some used DS games and a couple of them came without boxes and I'd like to get some of the boxes new ones would've come with (I'm OCD that way.) and I saw on store.nintendo.com that they would sell me official boxes just without the art. Is there somewhere beside eBay that I can buy the official boxes with the art?

Not with the art. As you saw, the Nintendo store will sell you (as long as you're in the US) a replacement box. However, artwork is harder to come by since 'replacement' inserts are not made. You have to rely on someone selling discarded/unwanted artwork inlays.

You could try somewhere like here: http://shop.bresoftware.com/nintendo-ds.html (note I've never used them myself and cannot vouch for them). Unfortunately it's really a hit-or-miss prospect.

Why not store them all neatly in a case? They can be in alphabetical order or by order of the franchise or something. It'd be a lot easier for you.

there are sites that have the boxart available for printing if you don't mind having to print your own cover inserts — just google them.

Instead of having to deal with a bunch of DS boxes why not just get a case that can hold a bunch of DS games, something like the one CN offered. I have one of those and when I do get a new DS or 3DS game the game card just goes in there and the box the game came in just goes in the closet. Much easier to carry a bunch of games that way.

While those are nice, I'm kinda (Biggest understatement ever) OCD about this, and it's why I buy most of my games new, but I only use those cases when travelling and I prefer the cases the games come in.

I'm in the same boat as you @SkywardLink98, Whenever I buy a game I usually buy it new, but If I see a game I want and it's a used copy, I must have the official box and boxart to go with it, other wise i'm not interested, even if it was a game like castlevania.
When you say you're kinda OCD, I know what you mean, I too get frustrated about how people don't take care of their games when they go to trade them in at EB games or on a website. Why must I see good games without their box/boxart?? it's just (sorry just a second......ARRRRRRGGGHHHH!!!) annoying, to say the least.

I'm with you guys.
I lost my copies of Mario Kart 7, Theatrhythm Final Fantasy and Dead or Alive: Dimensions and a part of me wants to track down the person who found them just so I can give them the boxes! D:

Well I can say that I agree with you guys at especially with the used game part which is one reason when I buy a new game I put it into my CN 3DS game case and the game cases go into the closet. That way if I do decide to trade them in I have the case and book to go along with the game.