I assume you mean third party fonts you've added? If so, pretty much anywhere you want.
There are already three Fonts folders on the hard drive they're at:
The first obviously belongs to the system. If you don't know what you're doing in that folder, leave it alone. The second is the Library you see when you double click the icon of the hard drive on your desktop. Any fonts in that folder can be used by any user account. The last refers to the Fonts folder of the active user. That is, whoever is logged in at the moment. Only that user can access fonts within their account.
It's not a good idea to activate hundreds, and especially not thousands of fonts at a time. They take up space in RAM when active. They more you have open, the less RAM is available for other apps. Long font lists in apps also very much slow down those menus.
I would create a folder for your fonts anywhere outside of the three locations I listed above. You can put is right at the root of the drive is you want, next to Applications, Users, etc. You can even call the folder Fonts if you want to. OS X will pay no attention to it, despite the name. It only automatically looks into the three main Fonts folders.
From there, you can activate fonts within that folder using Font Book, or any other third party font manager. If you're using Font Book, I strongly suggest using Library sets rather than normal sets. With the former, the fonts stay where they are (activated in place) rather than being copied into your user account (a waste of time and disk space).