I used to do the same, but I ran into too many problems with uninstallers. Specifically, I would try to uninstall an application and it would begin by trying to delete the start menu items it had created. Since I'd deleted 90% of the crud, those items were gone and the uninstaller would crash.
Of course, this is back in the 9x days. Have you run into this issue recently?
Never happens -- I install and uninstall crud all the time; no problem with uninstallers crashing if their icon isn't found. The only downside is if you move the icon the uninstaller won't find it.
I put all my Start Menu items in the same folder that contains the Programs folder. My programs folder then just contains the crud I haven't decided to keep yet or haven't otherwise organized.
I have ClassicShell configured so the class start menu appears if I click but the Win 7 start menu comes up if I use the keyboard (for searching).
Of course, this is back in the 9x days. Have you run into this issue recently?