1. Shrinking. First, this is a horribly cliche type of story. Second, it is pretty much impossible to do anything fresh with it. The characters get shrunk, deal with some tiny obstacles (usually including a cat or some other suddenly dangerous animal), and then get their size back. What else could you do with it?
How can I do it right? Have the character stays shrunken for longer than just an issue. It’ll push you to develop the formula in a fresh direction, and hopefully one more fertile than “and then they discover a microscopic civilization!”
2. Body-swapping. One character switches bodies with another, usually involuntarily. The drama usually comes from the characters having to survive despite having different powers or different roles than they’re used to.
How can I do it right? This isn’t necessarily bad, but it has been done extensively. It tends to work best if the characters have to keep their identities secret. If Jim and Luke can just tell everyone that their bodies have been swapped, it’s not really an interesting obstacle. But if Jim and Luke can’t talk about magic or the supernatural hijinks they’re involved in, then body-swapping makes it that much harder for them to maintain the masquerade. Give them difficult situations they can’t duck. For example, “Luke” suddenly has a piano concert and “Jim” is now the starting defensive tackle. The only way for them to protect the secret is to learn (or feign competence in) something totally new. Good luck!
3. Age change. The villain or an accident causes a character to get drastically younger or older (usually younger). This is even worse than shrinking because a hero turned into a baby is no longer a character so much as a prop. Also, these episodes/issues tend to be overwhelmingly cute. Ick.
How can I do it right? I’d recommend trying it like Big or Thirteen Going on Thirty or Seventeen Again. The story follows the character as he enters another stage of life. How does he handle his new predicament? That’s an interesting situation. In contrast, babies can’t do anything but cry.
4. World War II time travel. Time travel is not a problem in series that have been built around it, but “let’s do an issue set in World War II!” is shoot-me-in-the-face bad. The villains are one-dimensional, there’s no chance the writers will let the heroes lose and it’s cliche.
How can I do it right? Realistically, you can’t and I wouldn’t recommend it. However, if you’re dead-set on trying anyway, maybe try something more creative than sending the villain back in time to help the Nazis. One alternative would be having the heroes try to stop a well-intentioned “antagonist”–say, somebody who lost his family in the Nazi death camps–from going back in time to kill Hitler because killing Hitler might lead to Germany winning the war with a competent leader. This setup is stronger because the villain is more morally complex and because sneaking in to guard a hostile target is inherently more dramatic and challenging than an all-out assault. Also, the outcome is less guaranteed/predictable, particularly if the story is set towards the end of the war. Perhaps the story ends with the heroes and assassin agreeing to stage Hitler’s murder as a suicide, but only when the Allies’ victory is guaranteed.
5. Underwater adventures, particularly with Atlantis. It’s very hard to do an interesting aquatic tangent. Have you ever heard anyone wish that Aquaman or Namor would show up? Me neither.
How can I do it right? I think your best bet is to set most of the story in a sealab or a sealed city under the waters. The less time the characters spend in submarines or swimming, the better. Also, this kind of story might work better as a series focus than as a tangent. It’s not that aquatic stories necessarily suck (please see Finding Nemo or The Little Mermaid), just that an aquatic setting is usually a waste of time for land-bound heroes. Additionally, few land-bound heroes have powers well-suited to interesting underwater fight scenes, so it might help to have the climactic battle in a sealed environment like a domed city or in a coastal city above the water.
6. Saving helpless women. (Hat-tip to commenter Heather).
How can I do it right? At the very least, if she’s going to get herself kidnapped or otherwise endangered, maybe it’s because of something she did besides dating the hero? For example, in Iron Man, Pepper Potts endangered herself by sneaking into the villain’s office to steal his computer files. Sometimes Lois Lane is a competent investigative journalist. Give your characters a chance to be something besides just The Screaming Girlfriend. Maybe even you have some female characters that aren’t love interests! (A revolutionary concept, I know).
UPDATE: If you’re interested in plots that don’t need to die, I think this list of stock plots might help.