Several methods. For my 1/72 and 1/48 scale armor, I use a plastic storage bin like Deafpanzer's picture.
For 1/35 scale armor, I use old kit boxes and separate the spare parts basically by vehicle type. I have an old Sherman kit box that holds my Sherman excess bits, an old Tamiya Jeep box that holds my US wheeled vehicle parts, an M113 box that has my APC spare parts and an old Tamiya M1 box that holds my old modern tank stuff. Got a German box for everything German too.
I place a sticky label on the side end of the box and toss it on the shelf with my other similar kits. The label says "Parts" so I know it's not a kit.