Where the list of disabled fonts is stored depends on the version of OS X you are using.
First of all, the
~/Library/Fonts Disabled/ and
/Library/Fonts Disabled have never been used by Apple for the handling of disabled fonts; rather, fonts are simply deactivated in place: there's no need to move them out of the /Fonts/ folder in order to deactivate them. Those folders are most likely created by the Microsoft Office installer for Mac, or some other application installer.
As I mentioned, where the list of deactivated fonts is stored depends on the version of OS X you're using.
OS X 10.3:
~/Library/Preferences/com.apple.ATS.plist stores a list of file paths to the fonts which have been disabled in Font Book.
OS X 10.4 — 10.6: The enabled or disabled state of a particular font is stored within the font cache files themselves. There is no saved external record (like the preference file used in 10.3) of which fonts were disabled.
In OS X 10.7.x and later, while the enabled or disabled state of a particular font is still stored within the font cache files themselves, an external record of which fonts were disabled is stored in