Are there any
favourite command line applications that can be used to produce multiple sine
waves at once?
This should be in a FAQ... Theres a lot of programs that let you do this.
Yes, it can be done with Nyquist or CSound. Other alternatives are pd,
supercollider, clm, snd, galan, ecasound.
http://twiki.org/cgi-bin/view/Wikilearn/LA_SynthesisTools
But there are many others, Octave for example.
For the job you want, a graphical program such as pd, galan
or spiralsynthmodular might be the quickest solution. (others?)