I have a friend called Dean!
Unfortunately I don't think anyone knows.
AO and AE were programmed using the "ALIVE engine" which is probably closed source.
Levels in both games are most likely hard coded, as there is no level editor for them
3D videos were probably created in the latest graphics package at the time.
Nowadays people use 3D studio max, Maya, Blender... etc
It might say on the Oddworld Inhabitants website, otherwise... I don't think anyone knows.