I tried binders years ago, but they always leave the top of the cards exposed (on the top row) as they do not fit all the way down into the pocket and leave the cards susceptible to dings. Why Ultra Pro can't seem to fix this problem after all these years I'll never know. Anyway, I have 2 different storage methods depending on the year/value of the set. Both examples are shown below. Please excuse the bad photos - they were taken with my camera phone.
Here is my method of storage for a lower value set. This is a '78 Topps set in NM-MT+ raw condition.
The cards are placed in an 800 count box.
I use a spacer before and after the last cards to protect them from dings. These were from some Upper Deck (I believe) product that I got from my local card shop. He saves them for me and I use them for shipping or whatever.
Minor rookies and lesser HOFers are placed in penny sleeves.
Those are placed at the back of the set.
All cards are pushed together and held tightly in place taking up any extra space in the box. The cards should not slide. You can use waded up newspaper or whatever you choose. I've used plastic grocery bags in the pics below.
The major rookies and more popular HOFers are placed in Ultra Pro semi rigid top loaders and this is what it looks like as I close it up.
For more expensive sets, I place each individual card in Ultra Pro semi rigid top loaders and they are stored in vault boxes as shown with my 1954 Topps set below. If the set is too big for a vault box, you can always use the shoe boxes (2 row).
Any extra space is filled so that the cards do not slide.
The lid is placed on top and it is stored away.