Some people are not eligable for the indie lisence. Other then that I'm not sure of any other differences. Read the EULAs, they will tell you, I don't think they are that long.
An indie license is for a game that hasn't sold over $250,000
A commercial license is for developers that are going to exceed over $250,00
The indie is the same engine as the commercial.
Torque 3D Owner Tom Perry