Thinking how best to explain this, and I've decided the easiest thing for me is to just tell you what I would do. Someone may come along with a better method, but here goes.............
In the Documents and Settings folder, you'll see a folder for each user, and one for All Users. Lets' go to the All Users menu > Start Menu > Programs. Here you'll probably find folders for most program you've installed of your machine.
First make a copy of this folder to the desktop, just in case.
Then, what I would do is create a few new folders such as "Internet", "Tools", you get the idea. Then start moving shortcuts out of all those folders to the appropriate folder. While doing this, I would eliminate shortcuts I don't need/never use. As you clean out a folder, delete it.
This will probably take a while, but when done, you'll have a much more organized more programs list.
I hope this makes sense......