[Useless]

Go dual purpose on its ass. Continue cleaning it as time permits, but leave the link list pages in place. You can use the root index for your new project while still linking to the categories or main page somewhere down low so that the bots can continue to crawl them.

It was always a unique site because of its tons of categories. It would be a shame to see it go. Plus, if you killed those link list pages, those hits you do have would drop to zero within a couple of weeks - and that would suck balls. When you have time, you could always add some fresh/rotating content to the pages so that the bots will take interest in them.