There are so many to list, but here is a some of the software applications that get used in GYOML projects.
Graphics
Gimp [A great alternative to Photoshop] website
Inkscape [A great alternative to Illustrator] website
Audio
Audacity [A nice simple audio editor] website
Jack [A sound server that provides low latency connections] website
Hydrogen [A powerful sequence/drum machine] website
SuperCollider [Anything you can image can be done with this audio programming language] website
PureData: - An open source audio/video graphical programming environment. PD consists in a core environment and a world of extensions which provide functionality to do lots of different things like video , streaming, etc.
PD Software (Core App): http://www-crca.ucsd.edu/~msp/software.html
Commuity site: www.puredata.info
GEM (Video package): gem.iem.at
Interactive Graphics
Processing [A Java based graphics/sound/movie programming language] website
3D Software
Blender [A very powerful 3D package] website
Art of Illusion [An easy to use but powerful 3D package] website
Video Software
Kino [Digital video for Linux: capturing video and basic editing] website
Cinelerra [Digital video editor: still a little bit glitchy!] Official Version Community Version