Affiliated Sites
Amatsuki Livejournal Community - A fan community for Amatsuki where you can get scans, spoilers, the drama CD and all of the other fun stuff that I don't have here.
IsoParadigm - A new scanlation group working on Vassalord.
Bitter Sweet Scanlations - A large archive with lots of interesting manga, especially BL series.
Bliss Scanlations - Check them out, they do a ton of BL and historical manga (my two favorite genres...)
chibi R.I.P - A new site for manga scanlations, including Nanae Chrono. In Slovene.
Official Sites (Japanese)
A4 - Official blog/oekaki of Takayama Shinobu, creator of Amatsuki.
Vassalord Official Site - JP Release information for Vassalord.
Senki Senki Momotama Shoukai - JP Release information for Senki Senki Momotama.
Shuukan Shounen Magazine - The weekly magazine that Kyo used to run in.
Gekkan Afternoon - Monthly magazine that has Mushishi.
Shuukan Shounen Jump - Famous weekly magazine that runs Gintama, among other things.
Gekkan Comic Zero-Sum - Monthly magazine with Amatsuki.
Comic Blade Masamune - Monthly magazine that publishes Tactics.
Gekkan Comic Blade - The monthly magazine that carries Momotama and Peace Maker Kurogane.
Comic Blade Zebel - The quarterly magazine that Vassalord is in.
Places To Buy Japanese Manga
Sasuga Japanese Bookstore - A US-based store that is very friendly and will do special orders. Shipping is a bit slow, but they are also vendors at most large US conventions so you can catch them there.
Amazon Japan - Pricey shipping, but they sell everything and they're not too hard to order from in English. They're good for pre-ordering manga and for getting things that are out of stock everywhere else.
Kinokuniya - A bookstore chain with worldwide locations. Their online ordering isn't so hot, but there might be a store in your area. It's a great place to browse.
Fujisan - Not just a bookstore - they sell all kinds of stuff from Japan. I've never ordered from them myself but they're pretty popular.
YesAsia - Kind of like Amazon only the shipping is FREE to anywhere in the world as long as you spend US $25. But they don't always have as many manga pre-orders as Amazon.
Bookmart - Another used bookstore, similar to JPQueen. Their prices are usually good, and even if they don't always have things in stock it's good for browsing.
Book-off - My personal favorite used bookstore to shop in person because the prices are dirt cheap. There are locations in the US, France and Canada. And unlike most Japanese bookstores, they don't shrink-wrap the books in plastic, so you can preview before you buy. ^_^