How to remove apps from android market website?
Well, Now you CAN remove the unwanted apps from your market website as well as from the market history. All you have to do is delete from your all apps list.
Goto your play store app and select My Apps Then swipe the screen to your left to see the ALL apps list.
Just click the crossed circle icon (pointed with the green arrow) to remove the desired app.

Make sure you have uninstalled the app before removing. You can uninstall the apps directly from the All apps list as well.
Note: It seems that this list only contains market installed apps. (i.e. apps other than user installed .apk apps)