Back in 2005, Green Ronin published the Advanced Rulebook Series, a set of three books that gave new options for the d20 System. I mainly play Pathfinder these days instead of v.3.5, so have been rereading these books to determine how useful they would be for that system.
The Advanced Bestiary is a collection of creature templates designed to help GMs get more mileage out of their existing monster books. These templates range from very simple templates that can be added on the fly if necessary through complex templates that require a complete overhaul of the base creature's stats. (The book's most complicated template, the Amalgam, allows a GM to create a hybrid of any two monsters.) The Advanced Bestiary is easily my favorite Green Ronin title outside of the Freeport line, and of the three Advanced Rulebooks, it's the one I have used most often.
Green Ronin recently produced a new edition of the Advanced Bestiary for the Pathfinder RPG. All of the original book's templates have been updated (except for the handful that Paizo already published in their Bestiaries), and several new templates have been added. The new book is also in full color with all-new art, instead of black and white like the original. This is now one of my favorite Green Ronin books, period.
The Advanced Player's Manual covers a variety of topics: creating new races; six new classes; more uses for many skills; new alignment mechanics; mass combat rules, new spells; and an appendix with a new psychic class that uses skills and feats instead of spells. There are many good ideas in this book, but I have used very little material from it in my own games--just the planetouched template and a few spells.
The Pathfinder RPG has its own rules for some of these subjects. The Advanced Race Guide has detailed rules for modifying existing races and building new ones; Ultimate Campaign provides rules for mass combat; and Occult Adventures introduces "official" psychic classes for the system. (The Advanced Class Guide includes a warpriest class, but it is very different from the one found in the Advanced Players' Manual.)
Earlier this year, Green Ronin's "Pathfinder Short Cuts" PDF series included installments that converted some of the spells from the Advanced Player's Manual as well as the thanemage class. In a few cases, other spells already have obvious equivalents in Pathfinder (for example, water jet should be replaced by hydraulic push). But that still leaves a number of other classes and spells yet to mine.
The Advanced Gamemaster's Guide provides much advice for GMs on how to run their games, as well as a number of optional rules, complete with discussion about how those changes might affect the game. I've found the less system-specific sections to be a useful source of ideas (and reminders about how to be a better GM), but I have not used any of the new game mechanics in my own campaigns.
Much of this book's advice would be just as useful in Pathfinder, though it overlaps somewhat with similar chapters in the GameMaster's Guide and Ultimate Campaign. In addition, some of the variant rules already have equivalents in Pathfinder, such as Ultimate Campaign's rules for downtime and investments.
The list of "Forty Campaign Themes" has recently been expanded to fifty in the "Pathfinder Short Cuts" series. Other sections like this, which focus on adventure ideas and managing players, will always remain useful for Pathfuinder, and pretty much any other fantasy RPG.