I have to say - G1, Armada, and Animated are just about tied with me.
I love G1 because... Well, I think it explains for itself.
Armada has always had a nastalgic place in my heart.
And I love the new places Animated takes the storyline, even though it was short lived. Permalink
depends on your definition of "best". For pure nostalgia you can't really beat G1, but for writing, characterisation and quality of animation I think it's a battle between Beast wars, Animated and Prime for my favourite.