A good question and one I have been wrestling with and would like a better solution. So far, my preferred method is to purchase the 3x3 hard plastic sleeves that fit the TPG
graded coins in a binder. I then fill in the empty slots with whatever the coin is being stored, as my collection is a mix of ICCS, PCGS, NGC, 2x2 and Quadrum's. I like that I can easily flip through a series in order and not have to go through multiple boxes/page styles.
So far I have only done this for denominations that have a significant portion in TPG
holders (eg. Large Cents). I put most of my quarters in the black quadrum holders, which I really like. Unfortunately you can only fit about 45 coins in a 3" binder if using the 3x3 sheets, which means a full set of Canadian stuff would be well over 20 binders.
In a perfect world it would all be in the same holder, but not feasible in many cases, as the cost of a TPG
is multiples of what a common dime is worth. And for resale purposes, it is not the greatest idea to crack all your high value MS coins out of their holders.
The OCD in me would like them all to be the same, but I have a feeling it will remain a mix. My favorite is the Quadrum wood box with 3 inserts, it would hold about 60 of their square holders, but I was not willing to break all of my coins out of the TPG
holders to do it (not the higher value MS coins anyway).
Very curious to see what others do.