I have a pretty simple approach... don't know if it will help at all.

I capture on either my lappy or dslr.
All photos get transferred to my desktop PC (screen shot of file structure attached) to avoid clogging the lappy and dslr.
My astronomy photo directory structure is organised by year, then the child directory is names by date and target. All the images from that session are in that directory. That said, I don't keep my raw avi files from the web cam on the PC. I burn them to DVD. I figure if I lose the raw avi on the dvd I still have the stacked images, etc on the PC and backup disk. Not ideal I know, but the avis quickly occupy a lot of drive space.
I guess you could adapt this directory naming structure to work with different cameras, but it sounds like that's what you're already doing, so not sure my system will help you...

I guess I'm lucky since i haven't gotten heavily into archives of darks and flats, etc. (yet...)
All this is backed up onto an external HDD by SecondCopy every time my PC shuts down.
Al.