If you don't display them, I suggest putting them in sturdy deck sleeves and then in top loaders with the tops sealed off. That would be a great way to store like a 1st Edition Base Set collection.
If you're displaying your cards, then maybe you can try what I do. I put all of my cards in KMC Perfect Fit sleeves or UltraPro Pro-Fit sleeves, then I put the cards in regular UltraPro deck sleeves. I put the cards upside down in the perfect fit sleeves so the tops and bottoms are protected. Then they go into UltraPro binder pages and into 3 ring binders. All of my cards are stored that way and they've lasted the test of time. I also keep only 1 set per binder so the binders don't become crowded. Some people use Monster Binders to store cards as well, but I like being able to decide how many sheets I want per binder.
If you do not want to double-sleeve your collection, you may want to consider just putting your cards upside down in the sleeves instead then slotting them into the binder pages right side up. This protects the card from any dust that might get in.