Unfortunately, it does not appear to be possible (or at least practical) to only remove certain items.
However, if you want, you can reset the configuration and start from scratch.
Make sure Management Studio is closed, then delete or rename this file:
%APPDATA%\Microsoft\Microsoft SQL Server\100\Tools\Shell\SqlStudio.bin
Note that that file contains other user preference settings, so if you've customized your Management Studio configuration, you'll have some work to do restoring them.
Reference: http://social.msdn.microsoft.com/Forums/en-US/sqltools/thread/94e5c3ca-c76d-48d0-ad96-8348883e8db8/
Good luck!
