I've got a very weird hybrid system, and I'm also thinking about better ways to organise things:
2 folders, one for B+W, one for colour. The colour has sections for C41, C41 XP in E6, E6, and E6 XP in C41 (I'll need a new section for ECN in C41 soon too). This may get split into at least 2 folders one day.
In each folder are 10 sections, 24x18, 24x36, 24x54, 645, 6x6, 6x7, 6x9, 6x17, 9x12/4x5, and 8x10.
Then within each of these 10 sections they are sorted alphabetically by emulsion. ie APX25 comes before ATP, Delta100, Delta 3200, FP4, HP5, PanF, TMX, TMY, TX, XP2, etc, then in the order I shot them as 001, 002, 003 (god help me when I've shot more than 1000 rolls of anything).
All of these I've scanned, and the folders/subfolders on my computer are exactly the same as the physical folders, the final folders are called eg APX25 001, APX 25 002, with a 1-4 word description either of where I was, or what camera I was using/testing, eg "PanF+50 001 Weddings" has the pics I shot on the day two of my friends decided to get married, on opposite sides of town. So if I need to find a neg I generally search through my computer first, then I'll know exactly where it is in the folder.
It sort of works, even in the physical folders, because if I'm looking for something I can figure out what film I would have used. Indoor pics of gigs and poets? TMY if it's a few years ago, Delta 3200 now. Random street or travelling? FP4 or TX. High-res landscapes? APX or ATP. 617? RVP or Ektar.
I really wish I'd started off by dating things, at least roughly. I can tell on the computer what date I scanned it, but even that's not reliable because a lot of the time I learn something new about how to scan and go back and do old negs often. But I may as well start now.
I've recently started thinking about how to do certain projects, like I'm trying to photograph local poets for an exhibition. They span back many years on many filmtypes and formats, so what I've done on the computer is create a new folder, and then create symbolic links from there to the originals.
It sounds like this is sort of what you're trying to do, but without the computer/scanning bit.
What I'd suggest, to do this physically, is first to decide on a sorting scheme for the negatives, either complicated and convoluted like mine or just sheerly by date.
Then create some postcard prints of the good photos, even if they're only 4x5 (1/4 of 8x10), that's big enough to tell what they are.
When it's dry, write on the back in pencil where in the neg folder they are, eg format / emulsion / number / date / neg number (you can do a quick'n'dirty print, or get it all nice and then write grade / time / aperture on the back too).
These prints you can file by project, or subject, or whatever, then when you want to print it big you can find it by subject in the prints folder and look on the back to find out straight away where the original neg is.