Here's a fun shot I finished up today (had to put it on hold for a while since some client work came up). It wasn't actually made for John Deere Tractors, but we used their logo since it suited the premise of the shot.
Everything is completely cg (including the wheat field), except for the rolling hills and trees off in the distance (they're a projected matte)
Using a company logo without their permission is perfectly fine for a spec spot. We're not selling the animation commercially so it would be no different than someone modelling an ipod or a toyota or something.
but i guess it could be argued that if this aniamtion was the selling point to convince a company to contract w/ you that it might possibly be considered copyright violation.