A Maximized, Empowered spell does not have the empowered portion maximized. I think that's the only specific case of not stacking metamagic feats, it's debatable if that sets precedent for things like Split Ray + Maximize or is a single exception.
You are apparently allowed to determine the order in which the metamagic feats apply.
The FAQ has an example of a twinned+maximized spell effectively dealing twice max damage. IE: the spell is first twinned, then both instances are maximized.
Empower+maximize appears to be an exception to this rule.
So yes, I would say that you can combine metamagic feats with split ray, and they would apply to both rays. For example, a maximized, split enervation would inflict 4 negative lvs on both targets.