This situation happened in the last session I ran:
Evil wizard casts a Wall of Fire across the middle of a room. She's on one side, and the PCs are on the other. The party wizard decides he's going to cast a Cone of Cold through the Wall of Fire. My gut tells me this shouldn't work, but there's nothing in the rules that says it doesn't. People/objects can pass through the Wall of Fire (and take a bunch of damage doing so), so I guess a spell could also pass through?
Can a Cone of Cold pass through a Wall of Fire?
There is no written rule that says that area of effect magical effects block other area of effect magics. However, the two spells, by the rules, also don't interact in any way. The best your party wizard could hope for is to hit the evil wizard with the Cone of Cold and end his concentration on Wall of Fire.