I was really excited that the
Tome of Secrets listed the Warlock as a new class - I'm really hoping it's just like the WotC warlock with the serial numbers filed off.
Beyond that, I heartily recommend
The Practical Enchanter from Distant Horizons Games. The first chapter alone contains a spectacular breakdown of bonus types you can get from spells, and de-constructs them into variable "spell templates" that can be used to create thousands of new spells. And, oh yeah, it's completely FREE!
Monster Knowledge Cards from 4 Winds Fantasy Gaming fills one of those gaps you never realized you had until you check it out. It's standard operating procedure these days that PCs make Knowledge checks to see what they know about monsters, right? But the monsters in the SRD don't have Knowledge tables...until now. This is great for going back and giving the standard 3.5 monsters what later creatures have as a matter of course now.
Myth Merchant Press's
System Operational Reference Digent, better known as
SORD is a GM's best friend. This document completely reorganizes and gives a new layout to the SRD's rules for combat, making it INCREDIBLY easier to locate the necessary rules and speed up play. It guarantees that your combats will speed up by 10-15 minutes, and it backs up that boast. Also, for Pathfinder Beta players, there's
SORD Plus 1.0.
While it's meant for Modern d20, Pelgrane Press's
The Book of Unremitting Horror is one of the few monster books that actually frightened me as I read it. The writing, the art, the monsters...this book's tagline is "Because new times demand new nightmares" and it delivers those in spades.
Kobold Ecologies by Wolfgang Baur's Open Design has a dozen monster ecologies in a style reminiscent of
Dragon magazine. While these are from the pages of
Kobold Quarterly, this is a great resource if you don't have that magazine, and there's even some new material here. This book does a great job bringing to life the creatures it showcases.
Paragon Publishing has exactly a dozen products out, all of them for nature-themed characters. Ten prestige classes and two base classes are given, each one expertly detailing how the class approaches a different design philosophy for what it's meant to do. The design in these is great, and the flavor really helps evoke what's given. In particular, I recommend the
Shamanistic Warrior and the
Wildcat as great examples of what Paragon's produced.
The Random Esoteric Creature Generator may not be a "hidden gem" since it's published by Goodman Games, but it deserves mention nonetheless. This book works for all editions of D&D, and does a great job letting you build your own creatures. It also has superb advice on using monsters in your game. It just might be the last monster book you'll ever need.
Of course, if you'd prefer existing monsters that have been altered with advanced Hit Dice, class levels, and/or templates, then check out the works by
Creative Conclave. Whether it's
Goblinoids,
Orcs,
Savage Creatures, or something else, their Lazy GM line provides the stat blocks you'd rather not suffer through yourself.
Tricky Owlbear Publishing has released their
Behind the Spells series for a while now, wherein the history of various classic spells are revealed for the first time, along with new variants and related crunch. If that sounds interesting, the
Behind the Spells Compendium may be worth a look.
Steamworks: Deluxe Edition is one of those "you got tech in my fantasy" products that puts technology on an equal footing with magic (and psionics) in your game. It keeps to familiar rules for doing so, making the integration almost totally seamless, and does a good job explaining how it all works in-game as well. If you want to have a technological presence in your fantasy world, this might be the answer you're looking for.
Finally, this might be a tad controversial, but I want to recommend
Sisters of Rapture despite it being an erotic supplement (warning, the flash preview on the product link is NSFW). I want to say right up front that this book, unlike the BoEF, is actually good. Using actual artwork rather than photoshopped images, this focuses on a sex-positive cult instead of bombarding you with sex-based rules without any context. Mixing equal parts fluff and crunch, this is the erotic d20 book that gets it right.