My workable system is pretty simple. I got some BCW shoebox houses that I've organized all my trade bait and complete sets. The trade bait is by sport, by team. The sets are by year, set, and team. However, I take the cards from my PCs and my teams (Cubs and Packers) as well as the rookies from the sets and put them in binders. My PCs are all in binders.
In short, PCs and teams I collect are in binders, all the rest of my sets and trade bait go in the shoebox houses. I tend to keep most of of the cards in boxes in penny sleeves. I like the dividers of the houses because I can pull boxes out without having to move other things off the top.
Anyway, it's workable for me and I have noticed a lot less clutter since I got everything into boxes about a month ago. I hope I can keep it organized.
Thanks to everyone for the team collecting input. I'd love to hear more, if anybody has different ideas.