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I agree that if Congress couldn't stomach impeachment at a time when it still could have done some good, it's unlikely the Dems will collectively grow a backbone under a President Obama and bring Bush, Cheney, Rumsfeld, Gonzalez, et al. to justice. It's not just Obama who's inclined toward conciliation; the majority of the party has already shown it is more committed to harmony and business as usual than to prosecuting the Bushies' crimes.
One possible way to finesse this would be to have a Truth Commission keep a very low profile at first. It could do its initial fact-finding away from the cameras. However, it would eventually have to conduct public hearings - at the latest, when interviewing Cabinet-level and higher officials. Otherwise, too much secrecy would detract from its legitimacy.
Here's more fanciful - but not entirely loony - idea. How about subjecting these guys to one of their own tools: rendition. Let the Hague put them before a tribunal. There's ample evidence to try them as war criminals. I bet Cheney and Karadzic would have a lovely time as cellmates.