[kyuven]

Brainwashing is still in use, but it's harder to notice because, in order to do it RIGHT, it takes more time and effort than strapping someone to a table and injecting them with magic.
In reality "brainwashing" does exist, but the process involves ALLOWING the subject free will, and it's very important that they not be aware of the process.
Therefore, in a black and white morality universe where the good guys KNOW the bad guys are completely in the wrong from the get go, no one is truly able to be brainwashed because they'd inevitable be forced to do something that goes completely against their character. This is why mind control, possession, and forms of corruption are common in super hero genres.
On the other hand, in a more morally gray setting, where the heroes can be real jerks and the villains can be cheerful and friendly, it's possible for a villain to show a hero "hey, y'know what? We may be trying to take over the world, but at least we treat our soldiers like people! Want a cupcake?" Over time, they hang out and the hero betrays the jerks he/she once called friends in favor of the villain. Whether or not the villain remains nice, however, is up to the setting.
A good example would be Faith from Buffy the Vampire Slayer: The Mayor was evil and doing evil things, but he was nice to her and treated her in such a way that she was willing to kill for him.