Animetric.com - Shopping Guide

Based both in Tokyo and San Diego, J-List is the ultimate online shopping place for the Japan-o-phile.
J-List specializes in cute and unique items found only in Japan, everything from the yummy Japanese snacks and candies to collectible toys.
For those aged 18+, J-List also carries a wide array of adult-oriented toys, magazines, videos, and games. In fact they have the best deals when it comes to bishoujo (hentai) games.
J-List will ship out the items to wherever you are, which is a big plus against online shops that have territorial limits.

Right Stuf sells everything from anime videos to bishoujo games. They have a comprehensive selection of US anime releases, but they don't have much in terms of Japanese imports.
Looking through their catalog, you'd think they were just like any other online anime retailer. But what you should really be checking out is their Bargain Bin, which features original anime videos for as low as US$3 and there are hundreds of good titles to choose from.
Another section you should not miss: Weekly Specials! Want to get the whole Irresponsible Capt. Tylor or Boogiepop Phantom DVD sets for a mere US$50? The Blue Seed DVD collection for US$30+? This is the place. Right Stuf recycles these special bargains so if you miss one chance there's always another. The list changes every Thursday so don't forget to keep an eye out!
Yes, I have personally ordered from Right Stuf so I can vouch for their reliability. Probably the only negative thing about them is the rather slow processing to shipping stage. But if I you can get DVD sets for impossibly low prices then I'd say it's worth the wait.

Animenation has an extensive anime catalog that features both domestic releases and a chockfull of Japanese imports. They have an excellent selection of import anime and video game OSTs.
They have a section called Red-Hot Deals which features marked down items -- everything from graphic novels, toys, models, videos, artbooks, and soundtracks.
Animenation also carries Japanese snacks and beverages. Anyone for Pocky? Ramune? Pretz? You can order them here!
Good news for hentai fans, Animenation's selling Nutech hentai DVD sets at lower prices compared to other online anime shops.
Yes, I have personally ordered from Animenation so I can vouch for their reliability.

You'd be surprised at the sheer number and variety of anime titles they have in stock. Amazon.com carries both tapes and DVDs. They don't have hentai titles though.
Amazon.com is the best source of English-translated manga since they have the widest selection. They are also cheaper than bookstores or comic shops, tax-free to boot!
Amazon.com's pre-order prices for anime DVDs are pretty good, especially for boxed sets. They also have a section called Today's Deals, where you can get anime DVDs for about US$10 and up.
Amazon.com's customer service is fast, friendly, and simply unbeatable. Once they shipped me the wrong item, I received a replacement in a couple of days! Get this -- I live in the Philippines! They told me to keep the wrong item since it'd be too expensive to ship from where I was. You can't go wrong with Amazon. They really take care of their customers. In fact most of my anime DVDs were ordered from them.