I created an inventory program that allows me to organize by individual category as well as the entire portfolio.
The benefit of creating your own system is that it allows you to figure out the best way to catalog, inventory, and track things according to what's important to you. It also allows customization by category: how I organize ancients is very different from how I organize large cents.
For physical organization, it depends on the coin.
Regular or common coins go into standard 2x2 cardboard flips.
EAC go into 2" cotton liners, then into a 2" envelope.
Medievals & ancients go into a 2" cotton liner, which goes into a 2" envelope, which goes into a 2.5" poly flip. I print out general documentation in a standardized format on a 2.5" insert, and label the envelope with coin-specific info, pedigree, legends, &c. The 2.5" poly flip allows me to store previous collectors' inserts and auction tickets with the coin.
For an inventory code, I still follow the Dan Holmes method
