If you do boxes, have a cataloging system...this would be best for commons from sets and various players. Binders are great for viewing the cards that you have. This might be easiest if you have insert sets that you are trying to collect or cards that you want to use as trade bait that are low $.
I have a mix bag with most of my earlier player collections in binders, and most of my inserts in binders. My commons are in boxes. Most of my "higher end RC's, cards, inserts" are in hard or soft sleeves . Now, most of the cards that I have are in boxes, ones designated for jerseys, autos, inserts, and rc's. All "higher end or better than average" cards in soft or hard sleeves, including top RC's. All others, including cards for my player collections are treated like commons and placed in the boxes, sometimes in order, most times not.
I'd say, determine your collection, what you collect, how much you have invested into it personally and how you want to present your collection. Practicallity is your best friend...like gwheath said
Binders are nice but when you get 20 plus 3 inch binders storage becomes an issue.