Heh, that's kinda cool.
I've always tried to see if any custom covers from here were traded in to Gamestop, Blockbuster, etc. I've honestly thought of printing official covers for games I intend to trade to flea market vendors (as they actually care about that sort of thing and will offer more money for games in covers, unlike Gamestop), but I've been lucky enough to never actually need to do that.
If I found a custom cover of mine being sold (unintentionally) with a pre-owned game, it'd actually make me happy. It'd mean someone was actually using my creations.
On the other hand, if I got a custom cover with a game I bought instead of the official one, I'd probably be ticked... but, I'm kinda picky about that sort of thing. I returned Silent Hill 3 today moments after I bought it because I forgot to check to see if it had an instruction booklet. And now I need to see if I can return it again in hopes of one of the Gamestops having the music CD that was supposed to go with it. =P