Also, just figured this one out, if you want to deactivate an icon in the main app screen but without deactivating the application (so MeeFolders can still call it from within its own folder app and icon, for example), you can add the following line to its .desktop

EDIT. Marxian posted the latest version that enables you to rename .desktop files to disable the icon. But I'd consider adding this line to the .desktop file better practice than renaming it (as I had earlier suggested), because renaming the .desktop file could have unexpected consequences with other apps or with the system.

EDIT2: Doing it this way also has the advantage that the app icon will still be available inside Meefolders when you select a folder to add icons to it; otherwise every time Marxian releases an update you'd have to go through the tedious process of naming the .desktop files back again for them to show up in Meefolders when you recreate your folder structure, and then renaming them a second time to stop them showing up in your main app screen again.