I use Media Pro, each and every one of my finished, edited shots, is geotagged, titled and keyworded, all the metadata completed (copyright, author info, rights, contact details etc). The catalogue therefore allows me to search for a location, or theme.
Beyond that Capture One organises each shoot as a session, folders go:
Photos, Year, Description and Month (eg Sutton Bank Sunset October 2013).
Within each shoot's session folder there is a further hierarchy, Selects, Output, Deleted. Within the Output folder there is a subfolder for each output, eg full sized TIFF, full sized JPEG, small JPEG etc.
It sounds complicated but once you've got a workflow sorted out it all runs quickly. In life I am pretty disorganised but with my photos somehow I manage to keep it in order.