I have a problems with Storm since in some stories it was told that she can't use most of her powers in the small, closded spaces. Also, she isn't really flying (like Supergirl) but rather gliding with the wind, so she can't avoid the trap and make sudden moves. I'd try to caught her with then net or lure into the closed space, then attack from all directions.
Phoenix would be probably hardest nut, since she's a telepath and telekinetic user at once, so it's pratically impossible to surprise her (if you are not telepath as well), but I think here something like gatling would work fine. She could probably stop most of the bullets, but I doubt she would be able to stop all of them. And since she hasn't super strenght or endurance, she'd eventually fall.
For those with super strenght brutal fight usually works nothing, but there are things like chloroform or gass. But if our generic thugs are clever enough, they'd use one of them (female would work best) to act like a hostage. 99% of heroines would surrender in such situation. And it's priceless to see their faces when they understand that they were cheated.
Also, if the thugs are strong in number, they can attack and try to sexually stimulate her body enough to make her weak and horny. But with super strong ones, like She-Hulk, Wonder Woman or Rahne it would be dangerous. I still think that when you deal with a strenght, you have to use your mind instead. So, gas, darts, hostages and so...