For some reason, I get the feeling that the reason the top half of the 3DS is black for all the different colors is because other colors might effect the 3D effect. Anybody agree? :]

I was thinking of that also and I agree.

Maybe because black is the best choice color-wise as it stands out, and makes 3D look more striking.
You don't see any Blue or red HDTV's do you?

Hmmm. Well, it makes sense. So that's why 3D glasses are black.

Like I said in the 3DS Comes In 3 Colors Also 3DS Place Holder Site? topic:
I think it's because black has the best contrast to a bright screen, which makes the screen seem brighter and more colorfull. The same reason cinemas turn the lights off.
That's the reason I bought a black DSi, not a white one.
I don't think it has anything to do with 3D effect interference.

its just the prytotype, noone knows if final version will have the entire top half black.

Well, I think part of it at least is because is because the blue-and-black one looks awesome.

Just get a black 3DS