When it comes to managing fonts they can be like ants. Harmless by them selves but in large numbers can reak havoc on your speed and stability. The largest and most common mistake is to add a font to your system folder everytime you get a new one. Sure this will work but whatever OS you are using will have to load every font in that folder in to memory everytime your computer starts up and they will stay there until you shut down. This means your precious memory resources are being hogged by fonts you probably dont need every day. After too many fonts are added this way the system just starts breaking down and everything will run dog slow. Those are 2 very good reasons to use a font manager. You dont have to store your fonts in the system and you only have to load them when you need them. There are highly recommended applicationss for doing this: Suitcase from Extensis and Adobe Type Manager Deluxe from Adobe. I use suitcase but only because Adobe is no longer supporting ATM Deluxe (but the latest version still works fine).
The only fonts that should be in the system folder are the ones put there by installers. Some applications need certain fonts to work properly so they should remain in the system folder. (I had a barcode app that needed OCRA to be in the system folder in order to start up)
For everything else, make a folder called c:/FONTS and only load fonts from this folder. Whatever font tool you choose will make a record of where all your fonts are and just give you a list to choose from. If you move the actual font files they will not load properly.