I just organize my frequently used shortcuts into a folder, sorted into subfolders by category, and then define a popup menu that displays the contents. I access it either by hotkey, clicking on the desktop with a mod key, or by clicking on an xlabel "button" in my theme. Since I store the shortcut folder in the 'Links' section of my Favorites, I can also access it with the menus in any explorer window (just turn on the 'Links' Toolbar). Handy and flexible; you can drag and drop things in the explorer links toolbar and they'll be updated in your LS menus as well. Here's my configuration ($Favorites$ is defined for you in the core):

ShortcutsDir "$Favorites$Links\Shortcuts\\\"

;---[ Shortcut access via popup ]

*Popup "Shortcuts" !New !PopupShortcuts
*Popup "Shortcuts" "!PopupDynamicFolder:$ShortcutsDir$"
*Popup ~new