Well, every single one of the Complete Mage Reserve Feats is gives you a Su ability (Fiery Burst, Acidic Splatter, Elemental Summoning, Minor Shapeshift, and so on).
Thank you for pointing thouse out.
Most of the benefits from the Vow of Poverty (book of Exalted Deeds) are Su, and go away in an AMF.
That would be because all supernatural abilities are suppressed in an AMF - but they can't be dispelled nor are they subject to spell resistance.
I don't know if I'd say most, but some of the most useful of the scaling ones are (AC bonus, Exalted Strike, Deflection, and DR - with the True Seeing ability being the other Su one).
The ones that are Ex and thus not subject to AMF effects are:
Bonus feats (could be depending on the feat chosen), Endure Elements, Sustenance, Resistance (bonus to all saving throws and scales), Ability Score Enhancement, Natural Armor (also scales), Mind Shielding, Greater Sustenance, Energy Resistance (also scales), Freedom of Movement, Regeneration.