My collection isn't as big as Jane's, but I also organize by categories. In my kitchen (away from the cooking area), I have a large six shelf bookcase and a smaller three shelf one.
The small case holds my binders of recipe clippings and my Baking/Dessert cookbooks where I have these categories:
General/Compendium (the hefty ones!)
Specialty bakery/restaurant books (Chez Panisse, Moosewood, Macrina, Tartine etc.)
Chocolate (yes, I have a whole section of chocolate!)
Other single ingredient/single recipe type books (Lemon desserts, Berry desserts, muffins, cakes, ice cream, etc.) --I would have liked to include my bread books here, but ran out of room, so they are on the other bookcase.
The large bookcase has mostly savory (& mixed) cookbooks in these categories:
General/Compendium (again, the BIG ones!)
General vegetarian
"Healthy" (an obviously personal designation as healthy means different things to different people -- for me, this category kind of spills over from vegetarian, and then kind of runs into the next category...)
Seasonal/Local/Organic/Farm Market/Garden/Vegetable
Quick/Easy
Food personality/food writer/author-based books
Appliance books (slow cooker, grill, etc.)
Regional books (Italian, French, Mexican, etc. etc.)
Bread & other single ingredient/recipe type books (soups, etc.)
Preserving/DIY "project" type books
Holidays/entertaining
Misc. (a few random books that don't really fit well into any of the other categories or that don't fit where they belong (I try to keep this to a minimum!)
My shelves were a disorganized mess when I moved to my current home and unpacked them randomly just to get them out of boxes, but getting them categorized again has made such a huge difference! As Jane said, there is always some cross-over, but still makes finding what you are looking for so much easier.