I know a significant part of why I tried to avoid buying figures was because the places I saw had them way overpriced. (Japanese eBay sellers - though once a figure has stopped being made, I suppose they're really the only way to get figures....please correct me if I'm wrong. )
eBay is almost always overpriced and full of bootlegs. Very difficult to get an authentic figure and/or a good price there.
My favorite second hand shop is Mandarake:
http://ekizo.mandarake.co.jp/shop/en/Mandarake is a collection of Japanese stores that buy items from collectors and then resell them in store and through their site. These items are often unopened, and even if they have been opened, the figures are usually in excellent condition. I have found a few rare figures there at very reasonable prices (wayyy cheaper than eBay). Usually what I buy is marked as "box resealed", but when I get it I can't tell the difference between that and brand new. Since they are in Japan, you end up paying the same shipping as the sites in op.
The trick to using Mandarake is that they charge 500 yen fee if your order is under 5000 yen. Shipping and this fee is charged separately by store, not by order. I only place an order when I have enough items from a single store. Also, an item on the site may sell out that day in store, so there is a chance part or all of your order will be cancelled after placing. You'll get an email within 24hrs of placing your order. I always check the "cancel whole order if item is out of stock" for each item in my order so that my order can never dip below 5000 yen.
Another second hand Japanese shop is Jungle:
http://jungle-scs.co.jp/index_e.cgiI haven't used them yet, but I've heard only good things about them. It's the same basic idea as Mandarake, but you pay 5% fee for total order regardless of cost rather than 500 yen fee below 5000 yen. With Jungle, I don't think you have to worry about which stores your items are coming from, but not 100% sure.
-Edit-
Almost forgot, it's a good idea to search for a figure by its Japanese series or character name. Just find the figure in
http://myfigurecollection.net/, then copy/paste the origin or character Japanese text. You may get some results that you wouldn't with English text search.
Edited by lilman, 22 July 2012 - 04:42 PM.