The stores that don't ship outside of Japan include Yahoo! Japan Auctions (and other Japanese auction sites), Tower Records, and various Amazon and Rakuten marketplace shops. There are numerous other small independent shops. All these places have one thing in common: lack of information in English. If your Japanese is poor, I suggest translating the pages and item descriptions through Google Translate to get the idea of what the condition is like, edition information, missing components, etc. The translation won't be perfect, but it'll help you pick up some useful words. Some middleman websites have an automatic translation feature to help you out before you commit to buy.
I've used a dozen of deputy services over time, but there's no need to list the inferior ones. This brief list contains all you need. They all handle PayPal.
Noppin, the King of Auctions. They offer a separate shopping service for places like Amazon and whatnot, but the fees are little steep. There a better option for those, listen below. Like all the other services, Noppin charges a fee per auction, but it's only 500 yen for the auction value of up to 4000 yen. Here's a page listing all their surcharges and it might seem like a load, but if you read carefully and calculate, it's not that much. The bonus is that they hold your items in the warehouse for free for up to 60 days in case you win multiple auctions and want them consolidated together. Other services will start charging you extra if it's more than 30 days. Noppin also lets you bid in real time. Even the deposit process is automatic thanks to the pre-authorized PayPal deposit feature. And there's no need to deposit the total amount. Let's say you deposit 2000 yen, so with the multiplier of 3, you can bit for auctions of up to 6000 yen. Lastly, the search and bid pages all include an English translation interface. All in all, I can't recommend Noppin enough. Check them out.
Tenso. Check their fees: relatively cheap. The neat thing about them is that up until the item arrives at the warehouse, you do the shopping yourself. No need to send them a request with the link asking them to buy for you manually. Once you register, you'll be given a unique Japanese address (of a storage box with your name and account number within the warehouse) which you'll enter as your delivery address on a given shopping site. When it arrives at Tenso, they'll give you an option to request shipping to your home address, or you can wait and consolidate multiple items together using their consolidation service. Of course, there are weight restrictions and time limit of up to 30 days.
The only reason not to use Tenso is when the original seller doesn't accept foreign-issued credit cards (those shops don't offer PayPal to begin with). Or your particular card just doesn't work. I've never had this problem myself, but you never know. So far the folks on Amazon and Rakuten I've bought from charged my Canadian Visa with no problem. Same with Tower Records, except so far I've only bought from there within Japan, but still with the same Visa. But if you do have this problem, direct yourself to the following.