Being a big fan of the GI Joe line from the 80s (was a collector till some years but kept only about 20 mint-toys nowadays) and also a fanatic comic reade, I just have to show you this. A shame I hadn't thought of this earlier ;)
The "G.I. Joe vs. Transformers Dreamwave" mini-series
This series took place in its own continuity set in World War II. The Transformers & GI Joe's all had completely different which were appropriate to the 1940's:
Here, Cobra had discovered and awakened the Decepticons, reformatting their vehicle modes into 1940s era war vehicles and weapons. The two evil forces conquered much of Europe in an alternate version of World War II. G.I. Joe, here a group of American infantry men, find the Autobots who aid them in stopping both Cobra and the Decepticons.
http://www.yojoe.com/comics/tranjoe/