First some disclaimers I am a big fan of the Marvel sunbow cartoon series in the
1980's.  I did not like Sigma 6 at all watched one or two episodes and never
bothered again.  I enjoyed reading the marvel comic series.  I did not have the
entire run but read a big chunk of it.  I saw the live action film this summer. 
I liked it!  Because it caught the flavour of the old cartoons.  I give the film
3 out of 5.
Long ago there was a Champions supplement called Super Agents.  Which is exactly
how I see GI Joe and Cobra two powerful organizations at war with one another. 
Both 4th and fifth edition Champions have supplements for Viper the main villian
organization of the Champions Universe and for Until in one form or another.  In
the Marvel comic universe it is Hydra and Shield that are at war.  It is
possible for super heroes to work for or at least interact with such
organizations.  Viper has lots of super bad guys on the payroll.  Such
organizations can be a lot fun in any sort of super hero game.  They can act as
back up help for the heroes.  They can try to figure out the heroes secret Id. 
They can in many cases give the hero his powers or training.
They can be the heroes primary enemy or hunted always out to hurt the poor hero.
For the bad guys they are always coming up with crazy plots to take over the
world.  This alone gives the heroes plenty to do.  Then there are the spies the
traitors the double cross and other potential story lines.  Plus fancy new
machines that need wrecking before world conquest becomes a reality.  Well I
hope this helps improve your games.  Later all. Ferret.......