I find myself using quite a lot of a small number of books. Aside from the essential three, I find myself using almost everything from the Complete Class books, and quite a bit from Races of the Wild. On top of that, I draw heavily from the FRCS, PGtF, RoF, and MoF, because I'm currently running a FR campaign. Most of the other FR books see heavy use when appropriate; for instance, the party just entered Waterdeep for the first time, so that book is gonna stay open all session for quite a while.
I'd probably use the books mentioned less frequently if the players weren't absolute packrats for spells, abilities, and multi-class options. I have party members trying to go into a prestige class from all of these books (Bladesinger, Wild Mage, Thief-Acrobat, Contemplative, and Ruathar). Come to think of it, the cleric also is looking at Master of Radiance, so add Libris Mortis to the list. They have found or researched spells from all of the FR-specific books, and I like the villains to have the same flavor of spells, to add to the campaign's tone.
In the past, I've made do with a tighter reading list, but with 3.5 and the amount of player-accessible power and options, I find myself cracking open a lot of books every session.