I use FontExplorer.
ALL fonts are in Foundry. Then i have varying sets/tags for Serif/sans/script/display/glyph/slab/(similar to JatFlows list etc etc and any other description that makes sense to me for easy reference.
And then theres clients sets, and per job sets which can be handy when there's something similar (i usually delete these though)
Its takes time at the start, but is WELL worth it!
That said, the online font business has become so slick these day that you can go to MyFonts and just use their categories/search tools to find sets and then its just a case of whether you have the font or not :P