I have 3 folders of Fonts.
1)Installed.
You want this lean as it does impact system performance when it gets bloated.
2)Open source (GPL) fonts like you can get from
http://www.google.com/fonts/ (note: some link to Paid font$

)
3)Licensed fonts (only for personal use) that came with software packages (eg Corel Wordperfect 8 Pro)
Calibre will only find #1.
I embed #2 and #3 manually, includes makein the proper stylesheet entries.