I'm going to jump in on the "keep it all" stratgey:
Plate: can be re-used for another keyboard. Initially I had planned to use that rosewill plate I have for a 60%, but now I'm giving it to another GH'er who needs it for a project.
Case: You can put a phantom in a QFR case. I was unable to secure one and had to use the KB over cardboard. I would have use a QFR case if I had one.
PCB / switches / controller are all useful for custom DIY projects or to combine two broken keyboard to make one working one.
And of course switches / stabs should always be kept as they are interchangeable for most cherry keyboards and will be very useful for you or someone else to make customs out of.
I keep the caps just in case I won't have modifiers that fit, but nowadays I'm revising that as I have a few extra (nicer) sets I can use instead.