Comment 4 for bug 418726

> And you should leave it up to the user to decide if he needs that many fonts or not ;)
I was assuming you were using windows, where that many fonts installed is a really bad idea, and I don't think this is merely my opinion, as many other reports lead me to believe that Windows is not friendly with big font collections. I'm not sure about Linux/Xorg so might be completely different.
But even in your circumstances I would suggest you to use Fontmatrix (qt) for managing fonts. There is also Font Specimen (gtk). I tried Fontmatrix while I was using Linux and I liked quite a lot. It lets you manage your fonts in categories, activate collections of fonts with a single click, show information of fonts (type, author, encoding...), let's you compare fonts family, has a panose browser (used to search fonts by its looks, instead of by their names), package fonts used in a job for sending to a friend... and many many more features, it is really promising. Try it, I think it will help you.