Kruphix and Omnath, what color is the mana
You would have 2 green and 3 colorless.

Kruphix creates a replacement effect that applies to unused mana that would empty from your mana pool. But the text on Omnath modifies to normal game rules:


  101.1 Whenever a card’s text directly contradicts these rules, the card takes precedence. The card overrides only the rule that applies to that specific situation.


So because of the currently modified rules, the green mana doesn't empty at all, therefore the replacement effect doesn't happen for the green mana, only for the other colors.

If you had only green mana in your pool, Kruphix's ability wouldn't kick in at all, because nothing "would empty from your mana pool".