Here is a brief description of the programs I used in the making of the various different commercial projects shown in this demo.
For compositing, mask animations and 2D particles, I used Nuke and After Effects.
For Model, rigging, skinning, animation, lighting, simulations, shaders and render, I used ZBrush, Headus UV Layout, Maya, 3D Max, and Bodypaint. For some manual and automatic retopologizations I used 3D Coat. For the little programming I made, I used MEL and sometimes its Python translation. For most of the simulations, I used Maya Nucleus-based Particles, Cloth and Hair, besides Fluid Effects and RealFlow. For render, mostly Mental Ray and V-Ray.
For scripts, sketches, character development, character sheets, storyboards, concepts and animatics, I used good old office programs and some classics from Adobe, like Photoshop, Illustrator, InDesign and Premiere. Some Concepts I made with Corel Painter and some animatics with AnimeStudio Pro.
I used mostly MS Project and other management tools written for Linux environment. I translated the three PM stages (planning, execution and delivery) into the traditional three motion picture stages: Preproduction, production and postproduction. This scheme allows the biggest amount of modularity for this kind of projects because, at the end of the first milestone, you already know what the pictures are going to look like, which makes later changes superfluous.
If you want to see the technical demos (videos) you can find a list of links here