For me, it depends on what level of "post"-custom we're talking.
For figures that are done but not yet photographed, they either end up on a small shelf next to the table (short term--no more than a few days), or in one of those cardboard boxes they sell at Michael's to store photos in (mostly use that when I'm building several customs as part of say, a team, and want to do all the photography at once. It's very long-term storage). The box is the right dept for 3 3/4", and a piece of balsa wood strip squeezed inside makes a handy divider and brace to keep them upright.
After photography my customs end up on display, and that varies also. Currently I have two setups to keep some of them dust free, while others suffer:
Shadow boxes. I have 2 8"X12" shadow boxes than hold the bulk of my female customs. I have a third smaller one (not sure of the size) that holds three of my "masked villains"--Easter, Omega Elite and Omega Stormtrooper.
A fourth shadow box (19"x20") holds most of my other customs, at least the ones that'll fit in the narrow space. Balsa wood shelves are glued in to provide 3 levels of display, and I figure I can fit about 24 figures neatly. This keeps them all neat and clean and looks good on display.
Display Cases: I have three display cases, designed to hold footballs, that I use to handle my fantasy customs. Each also has one of the dios Cap made for me to act as a setting. Not a lot of capacity but again, they keep the customs dust free and like the shadow boxes, no loss of weapons or small parts.
I also like to use small, clear acrylic boxes for storing figures that either don't or won't fit into a shadow box or display; Michael's used to sell these but stopped (they can be found online). They're actually pretty neat, come in various sizes and in the past I used them instead of the photography box to hold customs long term.
Lastly I just store the remainder (mostly my Vanguard customs, my TEF customs, all my vehicles and my demons) out in the open, on shelves.
Some WIP customs (not finished but close) I tuck into storage drawers too, usually in the unit that holds my tools, glue, etc. (always end up with a few spare drawers); unfortunately they usually then get forgotten about.
