Every cloud has a silver lining, and even in comic books that's true. What are notable examples of this?
The one that immediately comes to mind is the original Thunderbolts. It took place directly after the awful Onslaught event and in the regrettable Heroes Reborn status quo. Remember, this was their attempt to "reboot" Marvel during financial turmoil, by segregating the Avengers and the Fantastic Four to another universe, one that was led by Rob Liefeld. The thought was that the Avengers and the Fantastic Four were no longer relevant in the '90s Mutantmania, and they would make them stand out without any mutants taking their thunder. It was as bad as you would expect.
In the main universe, there was a notable absence of the greatest heroes, leaving only mutants left, or street level heroes like Spider-Man and the New Warriors. Practically no big heroes in the world who could fight the big fight. This is where the Thunderbolts came in, to become the next great superhero team in honor of the Avengers.
Only they were actually the Masters of Evil in disguise.
It was a great story, one about villains getting redeemed as heroes (and one of Zemo's best villain stories) with it being like a reconstruction of the original Avengers concept, and one that could only be told in the status quo that was post-Onslaught, where all the revered heroes were missing. Not to mention that the Thunderbolts have lasted since then, as a Marvel staple. Look at how Screaming Mimi was just a D-list thug before, but a dark horse for Marvel after as Songbird. Likewise, Beetle was just a joke character to get beat up, but became a legit hero who was a lot more likable as MACH. As said, this was one of Baron Zemo's most memorable stories.
But yes, Onslaught itself was a bad story that made no sense, and Heroes Reborn was a terrible, terrible idea. However, it did give us the Thunderbolts, making that worth it I'd say. It helps that Kurt Busiek is way, way more talented than either Scott Lobdell or Rob Liefeld. It was kind of making the best of a bad situation.
Anything else to note?