The following is my list and it is limited strictly to 3e (anything in bold means I own it and the others I hope to find at con in February):
Airships (Bastion/Dragonwing): the title says it all.
Artificer's Handbook (Mystic Eye Games): An alternative system for creating magic items
Book of Iron Might (Malhavoc): A combat maneuver system that does not introduce new classes and also shows you how to build maneuvers. I also like the weapon styles
Elements of Magic: Revised (En Publishing), its companion EoM: Lyceian Arcana, and their sister, EOM: Mythic Earth which provide alternate skill based magic systems.
Experts/Experts 3.5 (Skirmisher Press): It re-examines the expert class, breaking it down into multiple NPC classes. It has new professions, and new alternate skill uses
Fewer Absolutes (Sean K Reynolds): two of three free planned web articles that re-examines immunities, specific spells, and trained only skills, their affect on the game and offers some suggested solutions.
Hot Pursuit: definitive guide to d20 chases (Adamant Entertainment) and it's companion, Hot Pursuit: On Foot . A system for handling chases
Libem Liboriam (12 to Midnight/Silven): a supplement on books and, iirc, libraries.
Magical Medieval Society: Western Europe (Expeditious Retreat)
Noble Steeds: A d20 Guide to horses (Avalanche): It's primarily about horses, but it does include other mounts. (There is also In the Saddle: Horses and Other Mounts (Dark Quest Games, but I haven't seen it).
Noble Wild (Skirmisher Press): Play awakened animals.
Poisoncraft (Blue Devil): A book taking a more indepth look at and expands upon poison (I know that Bastion/Dragonwing had Pale Designs: A Poisoner's Handbook, but I never saw it and Poisoncraft seemed to get more praise).
Psychic''s Handbook (Green Ronin): A skill and feat alternative system for mental powers
Redhurst Academy (Human Head): A wizard academy for DND. It is a beautiful book.
Torn Asunder (Bastion/Dragonwing): a new critical hit system for those wanting more detail. I have only seen it once and it reminds me a lot of the second critical hit system option from PO: Combat and Tactics.
Unearthed Arcana (WOTC)
Others include Alchemy and Herbalists (Bastion/Dragonwing), Ink and Quill (Bastion/Dragonwing), Guilds (AEG), Guildcraft (Bastion/Dragonwing), Toolbox (AEG)