Open-Source Software
I use GNU/Linux exclusively for audio. It is a free, open-source operating system, and one of the most mature and well-supported such systems.
I have tweaked my system for real-time audio, and I have assembled a pretty nice set of favorite open-source programs:
I use Debian GNU/Linux:Debian
With a customized 2.6.26 kernel:
Kernel.org
patched with Ingo Molnar's realtime patch:
Molnar's RT patch
For low-latency inter-application audio routing, the JACK Audio Connection Kit:
JACK
and I program using the GNU Emacs text editor:
GNU emacs
Also, I beg you, educate yourself about Open Sound Control:
OSC
(To free yourself from MIDI)
Some very useful information for doing what I have done:
Florian Schmidt - Linux audio guru
Music Software
Csound
Csound comes from a long line of music programs from Bell Labs. Free and open-source. It is a programming language for the creation and manipulation of audio. I challenge you to find something your audio software can do that Csound can't (hint: if it involves drawing notes on your screen, that's not audio software). Csound now provides a comprehensive API available from C, C++, Python, and Java. I have only begun to scratch the surface of Csound's riches, and I could spend the next 50 years happily playing with it. I hope to.
Pure Data
Badass modular graphical real-time audio creation/manipulation/analysis programming language. Free and open-source. Get one for your dog. You create little rectangles on your computer's magic light box and connect them with lines, and this tells the program what to do with the signals. If you can't do it with Pure Data then you're too young to do it. Created by Miller S. Puckette, genius, the brain behind Max/MSP.
Blue
A sequencer frontend for Csound, written in Java. Blue was specifically created for use with Csound, and it has dozens of revolutionary features for doing this. It facilitates the process of working with Csound immeasurably.