By what criteria do you wish to sort and organize them automatically?

I presently store all of my fonts on a USB key using a 'tiered folder system' I defined for myself and use NexusFont to browse and otherwise manage... NexusFont is only available for Windows at the moment.

Personally I find it intensely rewarding to manually sort, categorise and organise font files and data. I am particularly fascinated by the smaller details to do with formats, foundry/origin and encodings. Sorry, I know this doesn't really help you but I sympathise with what you are trying to achieve. For what it is worth I approach this kind of thing from a fairly linear point of view, sorting alphanumerically and then by family, origin, format and version. Good luck!

Id like to sort using the built in metadata in the font. I don't know what is the ultimate system of font sorting, but maybe Serif and Sans-serif at the top level. Then maybe Humanist and Geometric under Sans-Serif... I am guessing that there is no perfect solution for this. But which one is most common?

There is no "most common" format because designers cannot decide what criteria to use and which are the most important :D

The only method that is generally adopted as a data field in Truetype and Opentype fonts (so not in Type 1 fonts) is PANOSE. You might give this Javascript a try, it's one for Illustrator:

http://forums.adobe.com/message/4172363

and see if it works for you (i.e., you have a font in mind and are able to find it using the script). If it does, then the Panose information is enough.

Display and text fonts, condensed, expanded, extra-light or black, low or high x-height potential usage (books, packaging, greeting card etc.). It depends a lot on how you use the fonts to how you classify them (of course). Though I find the designations like humanist, transitional etc. interesting, I hardly ever use them to pick a font. The 'emotional' qualities of font are more important to me (friendly, rough, playful, neutral...)

I use Fontexplorer's classify function, to which I add a lot of own classifications. I sometimes use the smart set option to naarow down a selection based on some criteria (like: Serif, high x-height, text, low contrast)

If I might add to the question, I have a mac and I'm using Font Book to organize my fonts into different collections. I'd like to keep track of the different license files, since I have some free and some purchased fonts with different license types. Any suggestions?

I've used FontDoctor for years to organize my pool of fonts into a reasonable directory tree. It doesn't organize by category, but it does have options to organize by foundry and family name. It also does a wide variety of checks, conflicts, and repairs, which I think is useful.

It's now an Extensis product, available here: http://www.extensis.com/en/products/fontdoctor/index.jsp?ref=nav

I know you're not looking for a font manager, but I advise rethinking that line you're drawing in the sand. FontExplorer (by Linotype) is really good, and attempts to do categorization. I don't think it's very successful at that (as others have pointed out, it's a hard problem), but it might be worth a download of the 30-day trial. It does have a good system for both regular and smart sets of collections of fonts; I use that to keep track of, for example, all my OpenType fonts.

--John