I've been looking for some way to manage my links from within MT. So far, no obvious way has come to light. There are some kludges to use "Categories" but that seems fraught with problems. So I have started looking for non MT solutions.
At the moment, Linkster seems like it might do the job. I'll have to download it and give it a go ….
… We'll it didn't work too well (for me), so I've used an idea from Love links, which seems to work fine.