Neowolf said:
Characters taking just one rank in certain powers is definitely a problem. Here's a few that I've noticed:
Incorporeal
Flight
Clinging
Invisibility
Telekinesis (not as much of a problem, because there's a good reason to continue taking ranks)
Telepathy (because of low DCs)
The way to address this problem is to pay attention to what powers your players take and know when to say no.
Another way to address the problem is to admit that the PC live in a comic book world.

I know that might sound like "d'uh!" for a moment, but I have found that the more the players AND GM embrace the four-color world, the easier M&M gets, for example:
Incorporeal: In a comic book world, almost every villian has force fields that hamper Incorporeal as well as Super Intellegence to figure out a PC's weakness in Incorpreal (classic M&M newbie power player comment "You HAVE to pick a weakness for Incorpreal?). Even if a player picks Darkness as his weakness, you can have mystical villians come up who have Dark swords and the like.
Flight: With Teleportation, Super Speed and such, low levels of Flight end up being pretty tame in my game.
Clinging: What problems have you had with low-level Clinging? It seems that most levels of super strength can bring down any walls a man-spider happens to be stuck to.
Invisibility: Feats such as Blindsight, See Insvisible and even homemade feats such a Detect Thoughts pretty much make low levels of Invisiblity a poor investment.
Telekinesis:I haven't had many problems with TK, probably because most people who got it also had to buy extra because they wanted to do "death grip."
Telepathy: This is where being a Super Intellegent villian who does his homework in a comic book world pays off. "Ahh, I anticipate that do-gooder Mighty Mind will some how interfere with my plans. It is time I built or bought a telepathy resistant helmet, like Magneto has." Such villians also use blind contacts and drop off points to give their henchmen instructions on a need to know basis.
Now some powers like Explosion which at level 1 gives you Invisible AND Incopreal take a little more imagination, but it can be done.
And you don't always have to "go for the throat" on those who take only one level of something becuase they think they "busted the system." "Save-based" powers such as Suffocation, Stun and Dazzle can pretty give everyone a bad day across the board.
Don't forget there are also SFX based limitations and benefits. Make a Drain Bomb that is Extra: Area Effect, Flaw: Power Source Only (Mutation), if you have a mutant heavy game. And that comes to another tip you can use for any super hero game ...
Even though the two most widely known super groups (JLA and Avengers) showcase a group with a mixed bag of powers, most other super groups have some sort of theme (all teenagers, all mutants, all ex-cons, etc.) You know as a GM, it makes for an easier campaign if you have more adventure hooks, giving all the PC more common ground helps in this. How many times have the X-Men's biggest adventures focused on something that effected mutants world wide? A lot.
Heck, in M&M you have the prerogative to give the group an HQ so cut them a deal. Tell them if they can come up with a group concept you'll give them an HQ to go with it.