The fact that Maximize and Empower do not stack with each other:
1. Sets up a general rule that metamgic effects don't stack like that.
2. Does not in any way contradict Twin Spell from functioning on an Empowered (or Maximized, for that matter) spell.
Wipput is right, there are ONLY two ways this can work without contradicting the very plain language in Twin Spell.
1. Both the original and copy of the spell have the extra metamagic feat applied (empower, maximize, whatever)
or
2. Neither the original or copy have the extra metamagic applied.
I find it highly unlikely that you could do a Twin Spell and then be prohibited from using any other metmagic feats on that spell. Still, to make the feat compatible with 3.5, you could simply add in at the end "... when applying Twin Spell to a spell, no other metamgic feats may be used."
The other choice, which I find more reasonable, would be to allow metamagic effects in conjunction with Twin Spell.
I would not call either a "house rule." I'd call them both rules interpretations - not the same thing as House Rules at all.
Caliban's method of applying the Twin Spell effect of repeating the underlying spell only, excluding any metmagic effects is clearly in violation of the plain language of the Twin Spell feat and cannot be considered to be within the rules as written. The feat cannot be rewritten to support this without fundementally chnaging the feat, for the two spells would no longer be identical.
Caliban's method I would definately call a House Rule because it directly contradicts the language in the Twin Spell feat.