Personally, I would go by set and list alphabetically. That's typically what most seem to do and it's a perfectly serviceable way to organize, especially if that's how you store them regularly.

I would avoid trying to go by value; my current list is like that. From experience, with price changes and spikes, it's a lot more work to keep up than if everything is just sorted by set.

Generally, I don't like anything less than $0.50 anymore and just mention that I have junk rares under that value that I can look through for things people want.

I would order by color and put junk rares in a different area. Easiest to read imo.

I'm in the sac area as well. What shop do you usually play at?