My collection is fairly small compared to others I have seen (or heard about). I have just two drawers and some bookshelf space dedicated to my collection.
Probably more information than you cared for but here is how I have things set up.

Actually, this is more helpful for me as I am looking to move some of these things and down-size the collection.
Drawer #1
1600 count shoe box
- 1 row all my tradebait
- 1 row PC autos and RCs
3200 count monster box
- 2 rows Yankee doubles (O'Neill/Rivera/Bernie/Tino/Mattingly)
- 1 row PC insert sets, misc. team sets in snap cases
- 1 row empty toploaders, snap cases, fillers, penny sleeves
Drawer #2
- 800 count box with Yankees Topps cards 1950-1979
- 800 count box with Yankees Topps cards 1990-2010
- 800 count box with 2001-2004 GOTG complete sets
- 800 count box with non-sport sets
- 500 count box with "unsorted" Rivera/O'Neill cards
- 1990, 1991 Topps Baseball Factory Sets
- 2 wooden cigar boxes with O'Neill Autos/GU
Bookshelf
- O'Neill binder #1 (1986-1998)
- O'Neill binder #2 (1999-2004)
- Mariano Rivera binder
- 1986-87 Fleer Basketball, O'Neill YSL binder
- Mattingly/Bernie "basic set" binder