This HAS been discussed before, but I would have no idea what to search for. Somebody probably posted it on the homemade equipment forum and titled it "Help! I Don't Know What To Do!"
The important thing is what works for you and makes it easiest to put your finger on a particular moulding. The more you show, the harder this gets.
A long-time employee of mine, who was an excellent designer, liked to keep them sorted by color. I like to keep them in "families," providing the vendor's families make any sense at all. Sometimes we'd argue about it and I had to remind her who wrote the checks. Then she'd remind me who did most of the design. We should have been married.
L-J's families usually make very good design sense and I even hang the fillets with the rest of the group so I don't forget about them.
Some vendors don't assign any group names to mouldings and their burls, for example, will end up in the row with the L-J Kensingtons.
The smartest thing I've done with frame samples is to put a number at the top of each row. The same number is written (with pencil, since these things move around) on the sample's label and is also in the computer moulding database. Nobody puts samples away but me and it's easy to figure out where they go and find the next time.
I also have a rotating schedule - a row-at-a-time - of removing each sample, dusting it off, checking for damage and loose labels or velcro and ordering replacements as needed. It takes me a month (a few mintes each day) to get through all of them. Then I start over.
Sometimes I feel like Cinderella - before the ball.