In the Five-Episode Pilot, Snake Eyes is thought to be fatally irradiated. Major Bludd keeps the Cobra troopers from firing on him for this, and has a brief twinge of sympathy as he said he wouldn't wish what happened to Snake Eyes on his worst enemy, adding "Poor blighter."
In "Spell of the Siren", the Baroness is stunned when Cobra Commander decides to let a captured Destro rot in prison.
One of the more notable examples in the series is Cobra's opposition to selling drugs. In real life, narcotics are a major source of revenue for a number of terrorist groups. Moreover, in one episode involving a G.I. Joe/Cobra temporary alliance against a drug lord, a high-level Cobra officer has a personal grudge against said drug lord, and he gets Cobra Commander's support by explaining that they would be able to steal a large amount of money from the defeated drug lord's headquarters.
A comic book revival featuring said drug lord was portrayed in that version to actually be a member of Cobra, in charge of their drug-running operations, likely having to do with the fact comics!Cobra is much more ruthless and competent.
That story however does run contradictory to an earlier Marvel issue where Cobra Commander has a strong anti-drug stance and targets Headman out of a moral decision, rather than for money.
There's also Zanzibar, the self-titled Dreadnok Pirate. His profile claims he dabbled in river piracy, stock fraud and smuggling before being taken in by the villains, failing at them because they were "too much like real work". Regardless, his selfishness, knack for stealing from comrades, and awful hygiene make even his teammates hate him. And they suspect that his eyepatch is simply for show. (Zartan only keeps him on retainer to keep an eye on him.)
In "My Favorite Things" Serpentor proudly boasts of the many genetic templates that form him, referring to them as "conquerors, tyrants and kings". When a Strato Viper arrives and presents him with a portrait of Rasputin, he wryly notes, "Ah, Rasputin. What an evil scoundrel he was."
Storm Shadow is definitely not one of the good guys, but lives by his own personal code of honor that has seen him give up his objective or refuse to fight in order to maintain it.
