Aside from the archival thing, for me, the most important thing is finding the images after they're processed. I struggled with dozens of methods and settled on one that just works for me.
I store the negatives in PrintFile plastic sleeves most of the time. What I like about them is that you can make contact prints through the sleeves (I put the paper on the baseboard, sleeve on top, covered by a sheet of glass and expose the whole thing).
On an envelope
and on the contact sheet, I write a serial number (before contact printing... so the number is visible on the contact print)
Then, the contact print goes in a folder on the shelf. The negatives go in the envelope in a box (they could also be hanging in a file cabinet if you have lots).
But the secret to my sorting system is in the serial number. I used to go 1, 2, 3... then I started doing slide... and color negative... and the system got all screwed-up, overly complicated, just a big mess (especially when I accidentally skipped numbers and added letters to make it harder).
I thought about it for a few days and came up with the following scheme:
for right now, the number might read something like 2006-10-16-01
Year-Month-Day-Film number processed on this day.
The number of the film processed is usually quite small and easy to track (usually 01 or 02). I always put the leading zeros as it would change the way the serial numbers work (2006101601 is not equal to 200610161)
The contact sheets get inserted in the folder in order. New pictures can never have a serial smaller than their predecessor (unless I invent a time machine

) and I don't have to remember a thing. I don't even have to check where I'm at in the system!

If I have to take notes when printing a photo, I just add the frame number to the sequence. No matter what I shoot, I use the same system. When I shoot color film, I either ask for an index print or make one myself.
If I'm looking for a subject in particular, I just flip through the prints. It's easy, manageable and it works. Storing the contact prints with the negatives just didn't work for me... it's too hard to find things (which was very surprising to me).