A couple of others have posted about how they organize their collections so I thought I would too. I'm fortunate enough that I can use a spare bedroom in the house as my 'den'. We've got another spare bedroom for my wife, which she calls her office. This is a part of a table I bought at Ikea last year. On top of it is a two shelf thing I bought at Target. Before I had this set-up I had to haul boxes of cards out to the family room. Behind the camera is my desk and computer. I can easily roll my desk chair between the two. To the right (which you can't see) is a small table with my scanner.
The boxes you see with the cards are Velveeta cheese boxes. My daughter absolutely loves this stuff. I found out years ago that they are just wide enough to hold baseball cards. One box will hold about 225 cards. I use a lot of little yellow post-it notes to label the boxes. The top row of boxes have all the commons I bought in 2008. Most of the lower boxes have either Phillies, Astros or individual players I collect. I acquired just over 3,900 2008 cards (most bought, some in trade). That's more than I've averaged over the past few years and it probably has something to do with being involved with so many collectors on-line. I also bought something like 300 cards in repacks. And a bunch of other old cards (like the entire 1992 Donruss Studio set).
Above is a longer view of the table. I keep supplies like album pages and penny sleeves in the drawers on the far side of the table. The scanner is to the right. To the far left is a closet where I store all my cards. On the far side of the table is a new toy my wife got me for my birthday. Its a record turntable which connects directly to a computer through a USB port. It allows you to record old LP records (remember those) directly to mp3 files. More about that later.
At the end of the year, I put away all the cards I acquired that year. That usually means I put a moratorium on new cards until I get the ones I have away. I use these two-row boxes above. I mark the contents with post-it notes because I often end up having to shift cards depending on how many old cards I get. These boxes hold about 750 cards. I've got 25 of them which isn't enough. There are 3 larger boxes in the background. The two row boxes are nice because they are not too heavy. What goes into the boxes are what I call commons. A common to me is any card which is not a Phillie, Astro, one of the players I collect, or a representative card of a set.
The un-common cards go in this motley collection of binders. Player binders, Phillies and Astros binders, and a series of binders with representative cards (I call these my reference cards). I like 3" D-ring binders the best. In with the reference cards are any cards I have which book for over $5. If I ever had to evacuate the house, these binders are the ones I would take.
I've been seriously collecting cards since 1985. My organizing structure has changed several times as I think of better ways to do it. Part of the fun for me as a collector is the organization and cataloging of the collection. I use a computer database called FileMaker with custom built (by me) database files. I may share some details of that later.
In 20+ years of collecting you can amass a lot of cards. I currently own 76,802 baseball cards. I can probably put my hands on any one of them within 10 minutes.