After working with a batch and group approach to file naming, using a single increasing sequence number for images, I decided this was not going to be flexible enough. A little Googling led me to a great tool called "A Better Finder Rename" for MacOS X (download it here. It comes as a feature-limited demo, and a license costs $20. It was so immediately useful that I bought it. It will do pretty much anything I can imagine doing with filenames, such as adding or removing prefixes, changing sequences to a different range, etc. I also can imagine doing all this by writing an elaborate shell command involving "find" and "mv," but then spending the next few hours trying to debug it, and even then it wouldn't properly generate and pad the sequence numbers. This is a very well-thought-out tool!
Anyway, I'll describe the new structure, in the hopes that it might be useful to someone doing a similar project.
Groups, numbered 001 on, are used to describe, well, groups of similar photos. A batch of prints of the same size and and approximate age that look like they came from the same camera, or even the same roll of film and resulting set of prints, up to whatever level of differentiation you feel is useful. (As I discovered you can go a bit mad looking at the minor variations in yellowing and logos and stamps on the back of different photographic papers.)
Each group folder, which has a name like Group 001, gets a group.txt file describing it, saying something like "4x4 glossy prints with borders and annotations on the back in Marcella Armstrong's handwriting."
Within a group, create batches in the form of folders with names like Group 001 Batch 2007_10_20, for all the images from that batch you scanned on a given day. When you add a day, continue the numbers within the group from when you left off. Each batch gets an annotations.txt file with whatever notes you want to record for each image. Within that folder, the filenames look like g001_i001 and increase in order. So you can add to the group, but if you want to reorder the group or put images in the middle you'll have to do some careful renaming.
The benefit to this system is that groups are contiguous, but you can add to them later, if you come across more prints or slides that look like they belong to the same group. This is exactly what is happening to me. If all goes well, each batch folder also ought to be archivable separately, if you want to create some kind of backup organized by daily output.
Well, there it is... subject to further refinement!