I assume we are talking about the animated versions?
If so, I'd have to say that I prefer the G.I. Joe movie by default. The Transformers animated movies is such a load of crap (IMO - calm down, fanboys) that I can't consider it at all.
I watched it last year with my kids and I could tell that even they thought it was pretty lame. How fitting it is to feature Weird Al's "Dare To Be Stupid"!