I wrote this at 4.37 a.m. but I think it still mostly makes sense. See what you think.
Unless you're writing an adventure for general use, tailor it to the PCs and their power level(s). Put in villains and situations that these particular PCs are equipped to handle better than someone else might be. If one of your PCs is The Fastest Man Alive, some of the problems you throw at him should definitely involve doing things really quickly.
Crank the villains up. Generic goons are fine, but give the villains showoff names, catchphrases, visuals and power effects. These don't have to be good, either - the players in a long-running Marvel game I played in remembered Paste-Pot Pete more fondly than most of his gang.
Include escape routes for the villains. Let the PCs catch some and put them into the unreliable supervillain prison, let others escape due to taking hostages, let your mastermind fall into his own death trap which "nobody could have survived"...
Bear in mind the reactions of the public. Unless the PCs are "plain clothes" supers or "urban legend" characters, they should be on the front page of their local newspaper (run by a larger-than-life eccentric editor) frequently, booed or cheered by the crowds depending on their actions and other issues.
And they're not alone. Unless they're set up as the only superheroes in the setting, have some of the other heroes appear in crossovers. And if they are set up as the only superheroes in the setting, keep that status quo long enough that they'll be surprised when someone else manifests powers like theirs.
Decide if you're going kitchen sink or not. Even in a shared universe, Blade tends not to meet the Hulk or go to the Shi'ar Space Empire. (Although the former would be awesome...) And either way, ask the players for what kinds of future "issues" they'd like to see. You can add your own ideas and interpretations, of course.
And remember, above all else... everything's better with a monkey.