I say both, depending on the game, and I'm going to bring up some really out-of-the-blue points to support both sides. This is just something I learned in a class, so it's probably not even applicable here. XD
With the heroes on the left, they automatically have to face right. Because when we read in English, we read from left to right, which makes it seem like anything facing to the right seems to have an 'easier' time doing so. The same principle applies when loading up a graphic. If the left side isn't just a little heavier in color/graphics/whatever, we tend to see it as being unbalanced. We also see the left side first because that's the side we read from.
Heroes on the right side of the screen do just the opposite and our minds are tricked into thinking that there's some opposition, even if the random encounter is a rabid bunny.
Out of the two, I prefer left. I think that a lot of RPGs have the heroes on the right because a lot of big, commercial RPGs come from Japan, where they read from right to left.
This made a lot more sense in my head, sorry. ._.'