I've found two important self-reinforcing principles to be more important than the details:
* Don't let bare files exist at the "top level" (~), have a limited number of buckets
* All new stuff goes into an inbox (pragmatically, ~/Downloads) and gets REGULARLY moved over
Putting all the stuff from Downloads into folders takes <10 minutes if you do it once a week!
For me, the different buckets end up as either "browseable" or "searchable". For example, ~/ebooks is pretty sensibly organised into programming, fiction, etc., and all the files have human names, whereas I have a "statements/receipts/leases" bucket that's just a big bucket of junk that will hopefully pop up in search if I ever need it.