The Marvel comic run and the filecards are the basis of my Joeverse, but are by no means the limit of my Joeverse. Firstly, for me, the whole ninja angle is a dud. My Snake Eyes is a highly trained commando who happens to be proficient in several martial arts disciplines, but he aint no ninja. Storm Shadow is just a background Cobra intelligence agent. Cobra La never even existed, nor did V-troops. I tend to stick to the straight forward military stuff and ignore the fantasy influences. Transformers? Sorry, no. In my Joeverse Cobra invaded Benzheen, and Trucial Abysmia, etc, but the Joes killed in these storylines are all alive and well in my world. The Cobra Civil war took place, but Serpentor survived.
The cartoons never really influenced me as they were only shown here sporadically, and always seemed to be aimed more towards a younger audience. The DD comic lost me a few years ago and it never had any effect on my Joeverse anyway.

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"The future's uncertain and the end is always near." - The Doors "Roadhouse Blues".