Sorted by location (sort of, stop disappearing and running out of Zoids, stores!) for your shipping and import tax needs.
Japan
- AmiAmi
Often has good discounts…and has a whole lot of models and toys of a non-Zoid nature too. - CD Japan
has Japanese CDs, soundtracks, and DVDs aplenty—not just Zoids. Unlike Amazon.co.jp, they’ll ship many different ways. - HobbyLink Japan
HLJ also have a ton of other hobby items, hobby magazines, you name it. - Hobbysearch
I haven’t bought from them personally, but from what I hear they’re a good site for Zoids (and many other toys). - Mandarake
Sells items from their shops online and get in a lot of rare things—search on both “Zoids” and “ゾイド”. Be sure to check the item condition before you buy, as they’re sold as-is and opened Zoids are prettymuch at your own risk. - Yahoo!Japan auctions, Zoids category
Tons of items. The one downside? Even if you can understand Japanese, you’ll need a proxy service like Celga, Rinkya, or Shopping Mall Japan to bid for you.
Other Non-US
- Hobbylocus (eBay)
Another seller I haven’t bought from myself, but other people recommend. - Leoshop
I’ve never ordered from Leoshop directly, but I’ve been in on combined orders. Their Zoids stock is sadly dwindling, though they get in some new releases too. Possible warning: I hear that their shipping quotes have been rather odd lately. - Toy-Wave
One of the better-stocked Zoid sources these days, though that’s relative! Besides (occasionally incredible) deals, Ken gets a good amount of obscure and hard to find Zoids stuff in, even if prices may be high for rarities. - Yesasia
Often pricy, but occasionally not, and Zoids usually qualify for free shipping. Also has media (CDs, DVDs, etc.)
United States
- BigBadToyStore
don’t have many Zoids, but they get in a few new ones on occasion. - Image Anime
They don’t have a huge Zoid selection any more, but they get some new releases and carry some other modeling supplies. - Jedi Bill's Zoids (eBay)
Jedi Bill’s a collector and a reliable seller. Ask him if there’s something you want not listed, he may well have it. - Tatsu Hobby
From what I hear, Tatsu Hobby are a good place to get the HMM line of Zoids if you’re in the US.