Finally got to listen to one of the villain episodes of the BAMF podcast, and this grows from that. (If you don't listen to the BAMF podcast and you're reading this without being a close friend of mine, well, why not? I think it would overlap nicely with your interests.)
One of the problems with superhero games is that you don't get the backstory of the villain, and so the player interactions with the villains tend to be, "We beat'em up," and then the result is either "We won!" and they rarely think of the villain again, or "We lost!" and the players hate the villain and want to destroy him or her or it or them.
In superhero comics, however, the villains frequently have backstory that makes them more interesting characters with more complex relationships with the characters.
How to introduce the former into your game so they can have the latter?
Well, first of all, recognize that not all villains are memorable. Lord knows there are certainly more than enough disposable villains in comic books (I have heard rumours that Grant Morrison brought back the Eraser, and I am frankly startled, because a more stupid villain I cannot imagine). If most of your villains are forgettable, that's totally okay. We tend to remember that the Joker and Catwoman had early appearances in Batman comics, but for every pair like that, there are a dozen or two dozen villains who are forgotten. I love the Monk and Dala, who appeared in a very early Batman story, but they didn't reappear until the 1980s, about fifty years later. Hugo Strange was largely forgotten until the 1970s. So villains don't need a backstory unless they tweak the interest of your players. Heck, Magneto (as Dr. Tondro mentioned on the podcast) didn't even get a backstory until issue 150 of the X-Men.
One way to make a villain memorable and known is to give them an existence before villainy. We feel about Terra's betrayal because we spent issues and issues getting to know her before she turned on the players. I was thinking that, because so many villains are failed super-soldier experiments, you could do an adventure where the heroes are tasked with getting a set of characters to the government labs. The characters become NPCs to interact with. When they are finally given superpowers, one or two or six sessions later (it's long and involved because they have to avoid the bad guy hit squads) and some of them turn eeeevil, well, the heroes already have an investment.
Another way is to give them a flashback (as I was talking about the other day). It's probably easiest to have the villain as a pre-villainous NPC and the other characters are playing people trying to help but failing, but you can go whatever way you think your group will like.
A third way is to have a character or loved one of the players find the information out, talking to eyewitnesses. "Oh, yeah, Harlene Quinnzel, we knew she was abused but there was never any proof. We couldn't do anything about it. So sad that she died working at Arkham."
But again, you don't have to do any of this unless your players have already evinced some interest in the character.