It seems timely to remind us of this report from a year ago:

In 2002, as evidence of prisoner mistreatment at Guantánamo Bay began to mount, Federal Bureau of Investigation agents at the base created a "war crimes file" to document accusations against American military personnel, but were eventually ordered to close down the file, a Justice Department report [large pdf file] revealed Tuesday. -- NYT May 2008

The report also covers Iraq and Afghanistan:  See tables of Interrogation Techniques Observed, Tables 8.1, 9.1, and 10.1 (the pdf document is searchable). 
from the report:

One SSA who served two rotations as OSC at GTMO told us that he initially told the agents to write up detainee abuse allegations to a "war crimes" file so the FBI could retrieve the information if it was needed for further investigation.

 

Some agents were told to record such allegations for inclusion in a "war crimes" file; others were told to include the allegations in their regular FD-302 interview summaries; and others told us they were instructed not to record such allegations at all.

    

In general, these reports did not appear to have had a significant impact on military practices at GTMO.

On a related note, Torturing Democracy (link to part 1 of video) provides either a bland indictment or summary judgment of Bush Admin detainee policies, depending on how you watch it.