Each project was made from scratch from different software.
After effects is the primary software that was used for compisite, 2D animation.
Cinema 4D is the software used for creating anythng involving 3D. Modeling, texturing, animation etc.
Illustrator is a software used for drawing vector graphics. These graphics can be exported to Aftereffects or Cinema 4d for composite.
Photoshop is a software used for advanced masking and editing textures, bump maps and normal maps.