Any and all executive orders, so I understand, can be cancelled by Obama as soon as he is inaugurated. That would be a good way for him to hit the ground running.

In fact he doesn't have to wait until January 20th to effectively rub them out - every time such an order is made he could issue a press releasing confirming that it will be cancelled on the morning of January 20th.

Pardons are another matter. Perhaps in some cases there might be an option of taking advantage of the fact that presidential pardons for war crimes don't carry any weight outside the United States. I'm sure there are plenty of countries which would be happy to hold trials, especially if given a nod and a wink by the President. If the people facing the charges refused to attend, that needn't stop such trials going ahead in absentia.

Though, I wonder - would a court setup in Guantanamo be bound by such pardons, since that isn't actually in the States?