Ethics
In Slate, 3 legal ethicists claim The White House and John Roberts "violated federal law on the disqualification of judges".

Federal law deems public trust in the courts so critical that it requires judges to step aside if their "impartiality might reasonably be questioned," even if the judge is completely impartial as a matter of fact. As Justice John Paul Stevens wrote in a 1988 Supreme Court opinion, "the very purpose of [this law] is to promote confidence in the judiciary by avoiding even the appearance of impropriety whenever possible."

So, maybe Supreme Court nominee Roberts shouldn't have heard and considered arguments in Hamdan v. Rumsfeld while he was being courted by the White House about the high court vacancy. Needless to say, Roberts ruled in Bush's favor.

Roberts' vote was not a mere add-on. His vote was decisive on a key question of presidential power that now confronts the nation. Although all three judges reached the same bottom line in the case, they were divided on whether the Geneva Conventions grant basic human rights to prisoners like Hamdan who don't qualify for other Geneva protections. The lower court had held that some provisions do. Judge Roberts and a second judge rejected that view. The third judge said Geneva did apply, but found it premature to resolve the issues it raised. Hamdan has since asked the Supreme Court to hear the case.

Roberts did not have to sit out every case involving the government, no matter how routine, while he was being interviewed for the Supreme Court position. The government litigates too many cases for that to make any sense. But Hamdan was not merely suing the government. He was suing the president, who had authorized the military commissions and who had personally designated Hamdan for a commission trial, explaining that "there is reason to believe that [Hamdan] was … involved in terrorism."

Sure, he probably would have done the same thing no matter what. But you have to wonder--did that case come up in the myriad of interviews conducted around that time, before it was decided? Was the White House using Hamdan as a part of the interview process? Is there any question that, had Roberts indicated a problem with the President's argument in that case, he would have been passed over?