Here is what I do:
I put regular size packs in team set bags with a 3x4 top loader in the back for protection.
I put larger packs in graded card sleeves with a larger 3x5 top loader in the back. The bag is a little too big but seems to work pretty well.
What are you guys doing?
Interesting. I only have my stuff organized alphabetically. Looks like you take it a step further and organize by year also.