In Windows, you only use the Start Menu to start programs or access things not available in programs.
See http://windows.microsoft.com/en-US/windows7/The-Start-menu-overview for reinforcement. http://msdn.microsoft.com/en-us/library/aa511447.aspx#files says: "Don't put shortcuts to the following items on the Start menu" and then lists "Help files" and "Program uninstallers" among several examples.
Please only put a shortcut to the KDiff3 main program in the Start Menu. Everything else is available online or through the KDiff3 program. If you do this, you don't even need a KDiff3 folder in the Start Menu, enhancing usability by eliminating clutter and not burying KDiff3 inside a Start Menu folder.
+1 Bump
I would find this proposed start menu change useful.
I've tried just deleting the menu links, and it works, but you may get complaints from installers later.
I've tried applying the hidden attribute to the menu's shortcuts, but it's hard to get your displayed or not tweaks consistent, especially as we get further from the NT/4 base, version-wise