I saw it in both versions and the only things that the 3D really made ANY difference at all was the opening credits and the closing credits. Seriously. For this movie it's not worth it. I've seen movies where there is a difference but this one was most certainly NOT it.

CLARK: No. I'm just worried I'm a jinx.
JONATHAN: A jinx?
CLARK: Yeah. Let's face it, ever since she's known me, Lois's been kidnapped, frozen, pushed off buildings, almost stabbed, poisoned, buried alive and who knows what else, and it's all because of me.
-"Contact" (You're not her jinx, you're her blessing.)