I have 13 machines, most of them from the 50's, so I tend to group the feet by type of shank they fit, more than the machine they actually came with (or were bought for).
I keep types that fit on the same type of shank together, but beyond that they're usually just jumbled into a box or tin together with their kin. My 6600's box has a little slot for each foot but that's the best-organized set I have.
I don't seem to need to have them laid out separately from each other; as long as it's the right fit for the shank on the machine I'm trying to use I don't mind rummaging a little bit to find the exact foot I'm looking for. For me I'd have a harder time storing a large box, so it's worth it to have a compact jumble of feet to save space. It only takes me a few seconds to find what I'm looking for.
I don't have THAT many feet of any one type though; short-shank is the one I have the most of but I solve that by just keeping one set out that holds one of every type of foot I have; all the duplicates are put away in the cupboard.