So far as great homebrews go, I've been very impressed with Urbis and Amethyst, as well as Agyris (technically systemless, for the most part). There are also some great non-d20 settings that can be used with D&D, True20, or other d20 derivatives with little conversion. For example. . . .
I could see using the vs. Elves barebones setting (Balphor) with D&D, while the JAGS settings C-13 and Wonderland seem that they'd work well with True20, Core Elements, or even Classically Modern (a d20 Modern fantasy supplement).
Currently, I'm working on my own homebrew setting based on the Shining Force II console game (I really just want an excuse to implement SF-style save points in a tabletop game, as well as an excuse to play robots, birdmen, rat kin, and other oddball races).
Finally, I know that there is a largely systemless write-up of the Thief setting (plucked from PC games of the same name) out there someplace.