We have simplified modifier stacking in our games by means of streamlining the modifier types.
As for now, we use: Equipment, Situational, Dodge and Aura.
"Aura" modifiers are modifiers imposed by spells, spell-like or supernatural abilities. Each character can have just one aura imposed upon them. If a character with an aura already upon him is granted another one, the most powerful replaces the weaker. If both auras are equally powerful, the last replaces the former.
As it is now, we mostly decide which aura is more powerful on the fly (we don't care too much about number crunching, so the DM's (me) decision is generally accepted as the fairest one), but it would be great to have it codified.
Sadly, I'm too lazy to do all that work ;)