I'll chime in a bit.
I think it's important to think about the intent behind what you're organizing. My PC stuff is organized differently than the stuff I sell or trade.
I have my PC stuff organized in a few ways - low end cards are generally in nine-pocket pages in binders that are labeled with what's inside. My higher end stuff is sleeved/toploaded/team bagged and placed in a two row shoebox - I sort by player and then within the player they are sorted by year and brand. My vintage stuff is all graded, so it resides in two row shoeboxes but I just bought a few Sports Card Penthouses that will allow me to separate each year into it's own box. I think this will be a much nicer way to store things as I don't have to unstack boxes and remove lids. Everything of mine is labeled.
The stuff I have listed on eBay is all sorted by card type in shoeboxes on shelves - autographs, relics, numbered, parallels, inserts, rookies, base. All sports have their own separate place - because I am constantly selling/listing I don't make much effort to organize these boxes as that might be a continuous process. I do try and keep everything sorted by Topps/Non-Topps and I tend to try and organize brands together. I have a really good memory, so it's never too hard for me to track down a card.
My office is a big mess right now - I'm way behind on organizing stuff as I've opened a bunch of new stuff this month.