It was explained in the original line of comics that Cyclops possesses one of(if not THE) strongest projectile power in the universe that is wielded by a single mutant. Something to do with the fact that his power is actually coming through a portal in his head that links to a deminsion of pure energy. Hense the reason Sinister obssessed over Cyclops and the Phenix's offspring so much....
Good point (I admit I'm not a big X-Men fan so I'm not that knowledgable. ^_^)
Like I said before, the only chance Thor would have against The Phoenix Force would be to wield the Odinforce. But... that's not gonna happen.
There is NOTHING in the universe more powerful than the Pheonix. That is exactly why she is a running gag joke among the Marvel universe. She/It is just too damn powerful to keep around, but it always makes for a rejuvenating plot line.
The Pheonix controls matter on a molecular level, has masive telepathic control(to a degree), and has that awesome ability of being freaking immortal.
The only Mutant or Marvel character that stands a chance is Wanda, aka Scarlet Witch. She has that strange Hex ability that basically allows her to bend reality to her liking(when she really sits and tries).
If it were not for the Pheonix's anger management problems and Anger control issues, they would never stop it.