I believe yellow (thought reading) to ultimately be the most powerful, so I'd choose that one. You would essentially gain the ability to manipulate others and anticipate their motives/actions, which, in the right hands, should result in world-changing leadership abilities. The others are fun, but IMO at the end of the day don't have potential that is as far-reaching.

Flight and super-fast running would likely eventually result in death unless it was accompanied by some kind of invulnerability and superhuman reflexes.

(Regarding the edited quote)

-Red: As a particle, there is no fundamental difference, aside from boson vs fermion, between a photon and an electron or quark. Therefore, given that things composed of electrons and quarks are considered objects, I would assume photons are too.

-Yellow: Thinking of a new method--using mentally-assembled nano-objects, I could map out the exact areas which are equivalent to certain thoughts (which is proven, in concept at least) and then apply an MRI (using control over photons) to map out a person's thoughts using a nano-assembled (by me, mentally) supercomputer.

-Green: All I would have to do is look at, say, a tiger's DNA, match mine to it, and then rearrange my cells to match those of a tiger.

-Orange: Moving all particles away from me to create a vacuum (holding a small pocket of air immobile at my nose so I could breathe).

-Pink: Just move cells to the area and then cover it with a sheet of mentally-assembled carbon nanomaterial until it heals.