SBAgen

It doesn't seem like anyone knows about SBAgen, so:

SBAgen is like BWGen, but free. It's for Windows and Linux, and is harder to use for custom binaural beats than BWGen but just as good (steep learning curve for most). The advantage of BWGen is that it's a lot easier to learn how to make your own binaural beats and there's a fairly large community for downloadable beats - SBAgen doesn't really have much of a user community (yet!). You can get SBAgen at http://uazu.net/sbagen/ and get the trial version of BWGen at http://www.bwgen.com/

PM or IM me if you have questions about either, but I'm not an expert or anything.