This is a topic for stores that are not amazon Gamestop/Game and such.
This site may look ugly but trust me I never had a problem. This is a great Japan Import site with good prices and sometimes hase a buy 2 Famicom Games get one free.
Japan Game Stock
This is great website for retro collectors. ESP for systems like Genesis/N64/SNES as while you can of course buy the games but buy the manuals and boxes to other games. Lets say you have Ranger X on Genesis but need the box. Well if they have it in stock you can buy it. Not repro's either. Originals.
TradenGames
EDIT: Forgot one. Manny goes here sometimes.
Video Games New York
If you have any great sites feel free to add them.