I was asked about fonts and font-management by someone who “has tons of fonts.”

If you really have “tons of fonts” then that could be having an   effect on your system. I personally keep my -active- font   collection pared down to a minimum, and use Font Agent Pro to   activate other fonts as needed. For example, one seldom needs   “headline” (aka “decorative”) fonts active all the time, and those   constitute the bulk of most font packages. With software that auto-  activates the font only when it’s needed, you can remove some of   the sludge from the system during normal use.

Such font software will also check for font problems (and there is   also the excellent Font Doctor which does the same thing.) Font   book also has an implementation as well, although I”m not sure if   it will repair broken fonts.
Fonts are considered part of the operating system, and a damaged or   corrupted font can cause all kinds of mysterious issues. I’ve   experienced this over the years myself, hence my recommendation,   above.

I generally leave the Microsoft and Adobe font packages alone   (unless, of course, Font Doctor finds a corrupt font) and try to   keep my /Library/Fonts folder down to what Apple supplies and a few   others that are needed by specific software, such as the Britannica   et al. Equally, I try to keep ~/Library/fonts tiny too.

I do have some 1500 other type faces (many of which are “headline”   fonts) that I’ve acquired over the years (and have converted to   OTF, to stay up with OS changes) but these are all kept in a   separate folder, organized and activated only as I need them, using   Font Agent Pro.

(I was then asked about what was “the best” font software, to which I replied:)

Can’t reply as to whether or not Font Agent Pro (FAP)is “the best”  because I’ve been using it so long that I’ve not kept up with the  others.  If you already have software that is current and manages  fonts, you probably ought to use that, as I’d assume the differences  between packages is minor.

By way of reference, I have about 90 font-families / 140 fonts active  on my computer right now. FAP lists 4247 fonts in my collection (which  probably represent about 1200 families, I’d guess.)

As to using a font manager vs not: yes, it is far simpler to not use  one.

Changing from one manager to another isn’t particularly difficult, but  can be stressful if things don’t go right.
Generally they keep the actual fonts organized in a separate folder.  Changing then would entail uninstalling the software, and moving all  those fonts to (say) your user/library/fonts folder, and then running  the new font manager. The font manager will gather up and redistribute  the fonts according to it’s own needs.

That said, most font managers will let you create your own catagories  and arrange things to your heart’s content. Converting -that- from one  manager to another is pretty much impossible, if my experience is  telling, and a serious time-sink to convert.  For that reason, I  generally don’t bother; large type houses and grapic design firms do  bother.
Personally, I’ve found FAP to be more than adequate for my modest  needs, but, as I noted, that likely applies to whatever you have as  well. Just make sure you have the latest version before you go mucking  about.

As to how to proceed: I’d get a clean install of the system fonts from  somewhere, and move your /library/fonts folder out of the /library and  install the clean /library/ fonts.

Do that for your ~/library/fonts as well.

Then run the font management stuff, and include those moved folders.   As it is right now, on my setup, I have a “MyFonts” folder at the root  level of my hard drive.

hth