-Cobra is arguably the best one, or at least the most new-reader friendly. It's more like the TV show "24" than a Joe comic.
-Hearts & Minds is simply neat short stories fleshing out some back-story on certain characters. the first issue was quite good.
-A Real American Hero is obviously for the hardcore 80's fans. It should be riddled with continuity from the old Marvel series, and I'm ok with that, as I love the original run. In Hama I trust.
I'm reading them all, but I'm a sucker for all things GIJoe.
http://www.collectedcomics.com/gijoe.cfm