Hardly a complete list of 3rd-party gems, but here goes.
Fantasy
Fields of Blood – Eden Studios. Mass combat and realm management.
Torn Asunder – Bastion Press. Critical hits & fumbles
A Game of Thrones – Guardians of Order/White Wolf. Excellent d20 treatment of A Song of Ice and Fire. Snagged the rules for Influence & shock for my campaign.
Barony & Manor – The Forge. Great resource for staffing feudal manors and baronies with stock NPCs already made, along with a sample map/setting of the feudal realm in question. While I didn’t agree with all of the assumptions used, I found it a useful compliment to A Magical Medieval Society: Western Europe.
A Magical Medieval Society: Western Europe – Expeditious Retreat Press. THE d20 treatment of feudalism.
Grim Tales – Bad Axe Games. Streamlined d20 Modern for any genre.
Heroes of High Flavor – Bad Axe Games. Detailed treatment on elves, dwarves, and orcs/half-orcs.
Nation Builder – Troll Lord Games. One of the Gygax-world-building series. A great sourcebook for providing an in-depth treatment to your campaign nations.
Redhurst Academy – Humanhead Studios. Hogwart’s style school of the arcana ala D&D.
Toxicant – Mad Kaiser Games. Everything you ever wanted to know about poisons and then even more. THE definitive RPG treatment on poisons, anywhere.
Arcane Quarter – The Game Mechanics. A series of locales and NPCs that can be used in the default setting of the city of Liberty or can be used as desired for your own campaign city.
Unorthodox Classes – The Le Games. Additional 20-level classes for your 3.x game. Unorthodox Pirates is probably my favorite b/c it finally gave me a worthy swashbuckler class that could stand on its own.
Cityworks – Fantasy Flight Games. Excellent sourcebook for designing fantasy cities and running adventures and campaigns within them.
Crime & Punishment – Atlas Games/Penumbra. Law enforcement, investigations, justice, punishment, and imprisonment rules for your fantasy d20 game.
Love & War – Atlas Games/Penumbra. An excellent companion volume to Green Ronin’s Cavalier’s Handbook, Love & War focuses less on class mechanics and instead focuses on the 4 knightly virtues, how the various D&D races view knighthood, knightly orders, tournaments, etc.
The Kingdoms of Kalamar Atlas - Only useful if you're running a Kalamar campaign, but if you are, it should be treated as a core rulebook.
Divine Masters - The 3.5 rulebook on Kingdoms of Kalamar religions. In addition to the Kalamar fluff, lots of 3.x clerical crunch to grab. I used it to customize the religions in my campaign (which uses The Book of the Righteous).
Modern/Sci-Fi
Grim Tales – Bad Axe Games. Streamlined d20 Modern for any genre.
Blood-n-Space / Blood-n-Circuits / Blood-n-Guts – RPGObjects lines of supplemental D20 Modern rules. Not to missed. Although you may not use all of it, there’s plenty of good stuff to choose.
Modern Players Companion / Future Players Companion – The Game Mechanics. Since it’s not WotC, they’re not considered core, but dammit, they should be. Must-have rules for any d20 Modern or d20 Future game.
D20 Mecha – Guardians of Order. Fantastic vehicle construction book for d20 games.
Martial Arts Mayhem – The Game Mechanics. Kick-butt martial arts expansion for D20 Modern/Future games.
Future Armada – Ryan Wolfe. Hands-down, the best RPG starship deckplans in existence. Each is gorgeously illustrated, includes “action shots” artwork, deckplans, and pre-made NPC crews and ship stats for d20 Future.
For all the derisive cries of "inferior" 3rd-party products, and d20 "bloat", it was the 3rd-party publishers that brought me back to D&D and, more importantly, enabled me to tailor my campaign to my and my players' tastes. Plenty of gems out there and I keep finding more!
. I recommend Hollowfaust from Sword and Sorcery, its an excellent treatment of necromancy; Secrets of Pact Magic was mentioned earlier in the thread, both it and its companion volume (Villains of Pact Magic) are both excellent and available in PDF if hard copy is too pricey. The SFX skills series from UKG Publishing is well done (think Alternity D*M FX skills ported to d20), The System Operation Reference Document from Myth Merchant Press (what the Rules Compendium could have been or the worlds greatest reference document), finally I need to second Silverthorne Games Book of Templates Deluxe Edition simply great.
