For me all my sets are in binders, unless I have duplicates of sets. The duplicates I will put in boxes appropriate for the size of the set. Higher end cards, inserts, etc are in sleeves/top loaders and in a box reserved for them. Cards available for trade are sorted into sets and in large boxes. The exception to that is if I only have a couple of loose cards from a set. Random cards like that I just put in a binder reserved for those cards. My rule is if I have at least nine cards available from a set, it'll go in the box. Less than that I'll put them in the "random cards" binder. My player collection is made up of cards I intend to get signed so I keep them sorted by player, put into team bags and stored in a box for them. Once they're signed they get moved to an autographed cards binder I have.
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... including my list of hundreds of in-person or through-the-mail autographed hockey cards available for trade/sale!