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.
I took a 5 row monster card box and assembled it with only four rows which seems to fit the wrapped packs pretty well. I had some plastic tabs from hanging folders and put those together with regular top loaders to use as dividers. Here's a picture of the finished product:
I do the same thing for standard size packs. For oversized stuff like these I use comic book bags and boards.