Free
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.
Commercial
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.
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 find yourself loving SBaGen and making a lot of beats you might want to look into the features of NP2.
An incomplete comparison of editors may also be found on this [http://en.wikipedia.org/wiki/Comparison_of_brainwave_entrainment_software]wikipedia page[/url].