I started off taking my minifigs apart and sorting them by; heads, legs, torso, headgear etc. Then a year ago I had the urge to build them all back together as they originally came from TLG (with accessories) using all my set instructions. I placed each individual figure into a small zip-lock bag, which all go in one big box. At the moment I have most of them in their original form and some sorted into their parts so I can customize whenever I need to. As for the collectable minifigures, I keep them on their stands, those I will not mix (at least for now). Currently I am considering if I should take them apart again, as I can’t seem to make up my mind.
-TopHat