With a possible 500 combinations of plants, there's no way you'll be able to keep one of each seed in your seed trays. At some point you're going to have to discard some that you only have one of.

I am trying to keep one seed of all the "basic" plants, and keep a record of what I cross and what it gives me. That way, I can discard some of the crosses, and if I find I need them later on, at least I've got the "raw materials" there to recreate them.

And I also keep 15 of my highest-sellers for a quick money topup when I need it.