Special abilities: A Wonderful retains all the base creature special abilities.

Special qualities: A Wonderful lose all the trait from it’s previous type but otherwise retains all the base creature special qualities and gain Darvision 60ft, Low light vision, Damage reduction X/magic, Spell resistance X (see below) and Magical Claw.
I think you mean that a Wonderful creature retains its Special Attacks. "Special Abilities" isn't part of the 3.5. stat block. Otherwise creatures like the medusa would lose snakes and poison.

Special Qualities: what if the base creature already has darkvision 60 ft? Does this mean the base creature loses spell-like abilities or are those retained as well. What it has better damage reduction and spell resistance? Should it take the better of the two.

Debby

How does magical claw work for creatures that don't have claws?