As I download stuff, I just make sure that it has the manufacturers code in the file name and then put it into a general directory for processing.
As it starts to fill up, I have a .net application which is basically an IE browser with extensions. I log into JavLibrary, then point the app at the processing folder. It goes through each file in turn and takes me to the JavLibrary page, where I mark it as owned. It then pulls the description, rating etc off the page and I usually edit the description into something more meaningful, especially if I've watched it (and remembered it) by this stage. I'm more interested in the genre/plot than the actress(es), director, etc so I generally leave that information alone. When I'm ready, the local file is renamed with all those bits of data in it.
After that comes the organisation. As I've said, genre is more important than stars, so I have folders for teachers, secret agents, chiropractic massage, molestation, etc. I just move the files by hand into the appropriate folders. I have a favourites area as well, though, and also a "dump" area where I keep stuff I'm never going to watch again (probably) but also don't want to get fooled into downloading again (my memory is not what it was). this way I am not 100% reliant on JavLibrary either.
If I want to find a particular video on my computer, I use Effective File Search which is fast and efficient. If I'm thinking about downloading something, though, I usually go to JavLibrary to see whether I own it already first. This isn't a better search, but if I don't have it I can double-check any screenshots and sometimes the ratings (though they're very subjective and I often disagree).