I actually treat all my negatives equally, everything is filed by date with a date on it, and I have digital scans of all my negatives so that if I or someone wants a print I can quickly look at the scans and locate the negative by date. I also mark the back of my prints with the date so I can find them quickly.
The only thing I have that receives "Special" treatment are my Last Kodachrome slides, they are still in the boxes that they came back from Dwain's in, this is not to segregate them, but rather because I need more slide storage boxes. I don't store slides in carousels, but rather I keep them in archival boxes again sorted by date, but not all are scanned. If you want to look for a particular slide in my collection your probably going to have to watch a slide show because it's my photo and you are now my captive *L*.
Mounted Stereo slides are also kept in archival boxes that are labeled by Year/month and subject/occasion because it may take a few days to shoot a roll of stereo. For the most part I do not scan stereo slides unless I really need a stereo card, those get printed inkjet because I make really nice stereo cards. Again, if you want to see a stereo slide you can either sit through a slide show, or I do have handheld viewers. Either way, you are going to end up looking silly for my entertainment.