I think Van Jones nomination was withdrawn when it became clear he wouldn’t win a confirmation vote. But you’re right, I cannot think of anyone else.
Van Jones was an executive branch Green Jobs “czar”. He eventually resigned over his Marxist past but his position did not need Senate confirmation.
The following cabinet level nominees were withdrawn:
Bill Richardson as Secretary of Commerce.
Judd Gregg as Secretary of Commerce.
Tom Daschle as Secretary of Health and Human Services
The Senate has confirmed 307 Obama appointed federal judges and they have rejected six Obama nominees for federal judgeships.