SBaGen is a free open source command line program that allows you to create high quality binaural beats. Because it doesn’t have a GUI it might be hard for some people to master right away. But in my opinion it is the best binaural beat generator out there because: 1. It is still in active development. 2. It has a large user base and 3. It is very powerful. Cross-Platform.
Gnaural is another free and open source application for creating Binaural beats, but unlike SBaGen, it runs in a GUI so it might be easier to learn. It has support for infinite layers (or voices). Last update was September 07. Cross-Platform.
Bwgen is an old commercial binaural beat program that does have a GUI. Because of its age has a rather large preset library, but in my experience is harder to program than SBaGen, though many people prefer it because of its GUI interface. Windows only.
TransparentCorp has the most selection and probably the best applications; applications like Neuro-Programmer 2 Is an actively developed high quality commercial binaural beat generator that has a couple of features SBaGen doesn’t (isochronic tones, minural, GUI, ext). NP2 has a great graphic interface and is very powerful but my only problem with it is that it is windows only and proprietary ($50 and requires a license for commercial use). If you have a PC and want something with the power of SBaGen with a graphical user interface you might want to look into the features of NP2.