Lincoln ignored Chief Justice Taney's order to cancel the suspension of habeas corpus during the Civil War. Taney was then sitting on the United States Circuit Court for the District of Maryland. The justices of the Supreme Court traditionally sat as circuit judges while the Supreme Court was not in session.
See here:
http://en.wikipedia.org/wiki/Ex_parte_Merryman
Yep, I remembered that one, but it wasn't the Supreme Court decision I was looking for.