Four six-foot bookshelves for my books. 1 bookshelf for my mini's.
When I need to carry more than 3-4 in a backpack I have always used milkcrates.
Milkcrates were also my storage of choice until I owned my own home and could have bookshelves.
Bookshelves for the most part. Lesser used ones in the basement, more frequently used ones on the shelf under the nightstand or when that is full on a pile on the floor. My travelling kit is kept in the backpack I use to head to games with. Makes it handy to haul the really frequently used books to the Living Room too....
Currently all of my gaming books are stored in a large gray plastic tub with a lid that I got at Wal_Mart for about 4 bucks. All of our books were stored in about a dozen of these things, and each of them weighed upwards of 100lbs.
Boy was that fun.
My gaming-books-tub is currently being used as a printer stand. Which shows how much gaming I've done in the two months since I've moved. Hopefully that'll change soon ... if I can convince my wife to let me make a 45 min-each-way commute once a week to game.
Back when gaming involved going over to a friend's house for a weekend, I had (still have, actually) these heavy duty plastic file boxes I would use. They had pretty strong hinges, and the front was a snap-tight clasp with a metal bar that went around part of the lid to hold it down. As I said - pretty sturdy (to hold various AD&D or Car Wars books) and I've still got the dang things.
We keep ours on a bookshelf. Since we live in Florida we also have a cooler that fits all of the books so we can keep them with us and safe in the event of flood or hurricane.
Lots and lots of bookshelves. For transport, I've got an old laptop computer "sleeve" (it's a zipped bag, but "sleeve" gets the image across better) that is just perfect for 3-4 books.
The books I use most often (every game night for example) I keep in a backpack along with dice, note cards, and my most commonly used minis. Everything else is kept in a large plastic tub with a lid.