I've included links to places like Amazon Japan and Yahoo! Auctions Japan (YAJ for short), but ordering things from these places can be kind of tricky.

Amazon Japan: Ordering from Amazon Japan isn't too bad, but you might be scared by all the Japanese text at first. But fear not! On most Amazon Japan pages is a link you can click that will turn a lot of the site's text into English for you. The other thing you'll need to know is that 1. Amazon Japan can't and won't ship games outside of Japan and 2. if you're ordering a used item, not all sellers will ship internationally. But otherwise Amazon Japan is a cinch to order from.

Yahoo! Auctions Japan: This is an absolute treasure trove of MOTHER merchandise. Sadly, it's not very convenient to use if you're not in Japan. Most sellers won't ship outside of Japan and will probably be freaked out if you ask them a question in English. If you're not in Japan and don't know Japanese, then you'll need to use a service like Celga that will bid on stuff for you and then ship you the stuff once they receive it.

For more details and a more comprehensive list of go-between services, check out this page on Game Swag.