These are all the links I use regularly when shopping for components. The majority of them are in japanese but I hope they can help someone.
Edit: Added Strawberry-Linux
My first stop. I buy my servos and most other stuff here.
They have a great variety of electrical components and kits although the selection isn`t great. Their discount sections "100 yen" and "outlet" are a good browse. Cheap AVRs butuser again not a good selection. Plus they have the Sharp IR sensors for $4 :)
Based in Japan and they don`t ship international.
Sengoku Net 千石電商
I don`t use them much but they have some decent stuff. Electronics plus a small selection of mechanical parts like gears and motors although the prices for those are ridiculous.
Based in Japan and I`m pretty sure they won`t ship international.
Marutsu Parts マルツパーツ
A much better selection than Akizuki but the prices aren`t as good. Sign up for a user account and you get reward points for purchases.
They are based in Japan and don`t ship international.
RS components アールエスコンポーネンツ
Excellent range and service, but you pay for it. A bit like Digikey or Mouser. Everything from plain old resistors to specialized industrial stuff.
They say they`re international and have localized websites but I don`t know where they are based. I used them once and the shipping inside Japan was only about $5 so they probably have a local warehouse.
Haven`t used them because the website sucks. They have a decent range but trying to get any kind of information out of it is painful.
Original Mind オリジナルマインド
I love browsing this website. I`m expecting my keyboard to die soon because of me drooling all over it.
Mechanical and electrical components. CNC kits, linear slides, ball scews, bearings, mounts, motor controllers, end bits, you name it. Hobby CNC builders dream website. I just wish I could afford it all.
I get their newsletter and browse the recycled section weekly. My wife puts on her worried face when I look :)
Tsukumo Robot Heaven ツクモロボット王国
Robot kits. Expensive robotic servos etc. Never used them.
Robot and science kits, plus toys and games. Again, never used them.
Strawberry Linux ストロベリーリニックス
Good range of imported "western" stock like Arduinos and Sparkfun products. ４００円 delivery fee inside Japan.