lxpanel populates its menu with the .desktop files in /usr/share/applications. An easy way to prevent an app from appearing in the menu is to edit its <app>.desktop file and add the line:

NoDisplay=true

If you've already got NoDisplay=false then change it to true. Save the file, kill and restart lxpanel and there you go; menu item gone. Thanks to skottish for this handiness. Although, I didn't cp any files as suggested. We all have our own ways of doing things ;)