Getting rid of a folder can be quite time consuming, depending on how many applications it contains. If there are just 2 or 3 apps then it isn't that bad, but 5 or more can get pretty tedious.
That's because to delete a folder, you must first drag every application from the folder back to the home screen. After the last app is removed, the folder deletes itself. A new utility is coming to Cydia though, that could change all of that...