If you liked Avengers: Earth's Mightiest Heroes did you also see any of Iron Man: Armoured Adventures which was airing at the same time? I know that a lot of people never gave the show a chance because of the teenage Tony Stark angle but Armoured Adventures had a couple of really great Doctor Doom episodes, both in the second season. Plus, the voice actor for Doom, Christopher Britton, went for a vaguely Eastern European ascent this time around instead of the more typical aristocratic British, which was a nice touch.
In terms of Doom stories to collect I highly recommend the original Doom 2099 run. The Warren Ellis trade is out of print but still relatively easy to find, containing the middle part of Doom 2099. The earlier issues and the few after Ellis can still only be found in their original floppy prints. If you feel like a challenge it's worth it to collect the whole series. Doom 2099 is classic cyberpunk at its best; dark, dystopian and truly an intoxicating spectacle to behold; in a world so messed up Doom emerges as the hero by default and so he sets about saving the world as only Doom can.