This is the continous bane for me in card collecting. I go back and forth between what I want to do. I currently have my entire collection neatly in 3200 count BCW boxes on a wire shelf at home. I don't use any sleeves or toploaders or anything. They are just placed in order in the boxes and I use the BCW Monster Pads to keep everything secure.
I used to have cards in toploaders for more valuable cards, but I didn't like that they were seperate from the rest of the set. I also couldn't come up with a good system as to what went into a toploader because inevitably something would come along and mess it up. Basically I had rookies of All Stars and Inserts/Parallels of All Stars in toploaders. But I found it silly that a SSP base card wasn't in the toploader box even though it is more valuable than the vast majority of inserts I have. Also, I saw flaws in the system like having a BJ Armstrong rookie in the toplaoder box over a Marcus Camby rookie. Sure, Armstrong was a 1x All Star but a guy like Camby had a better career even though he never made the All Star Game.
I have also been told plenty of times by a very experienced member that plastic can eventually attack your cards.
Another thing to consider is that supplies are expensive and take up a lot of room. Using the method of storing all my cards in 3200 count boxes keeps costs down and saves a ton of space.
I am currently considering putting all of my complete sets in their own binders, but I haven't really committed yet. Just another day of trying to figure out the best way to store these things.