I'll second supercollider, I've heard some very interesting things done with it.
But by far the most useful program you could probably use for either synthesizing sounds/music or manipulating existing audio that you have the rights to use... would be a combination of a DAW (digital audio workstation, such as cubase, pro tools, ableton, cakewalk/sonar, etc) and either PureData or MaxMSP.
PureData and maxMSP are OOP environments that are interpretive much like unreal's kismet and/or material editor, based on patches.
Puredata is opensource and free. MaxMSP is the same program with a few more bells and whistles, but it is a commercial release and costs quite a bit, unless you're a student. ( I got it for 250 USD ) but PureData will do everything MaxMSP does, it just doesn't look as nice and not quite as user friendly.
On the other hand, if you have a mac available Cecilia (http://www.csounds.com/cecilia/)) is a great program. It is a frontend for Csound, so if you have any Csound algorithms you can plug them into Cecilia and get a good idea of what they are doing. It comes with a bunch already installed I believe, The author doesn't feel like supporting windows, however, so the port to windows is done by a 3rd party and is very buggy.