It is a typical sign of an active forum. And WOW, I think yours sets some kind of record for the number of categories and forums within each.

Disk space has little to do with it.

Are you noticing slow responses to http requests?

I take it you are on a dedicated server? A Pentium 4 is a bit dated, but can handle a good load. It might be that you are hitting it's limits if your site/forums are truly very active.

There are tweaks you might be able to do to MySQL to help out, but I am thinking that you might be bumping your head against a hardware limitation.

Others likely will have better input.