Bill Clinton could have won a third term, but his heart condition was such that he probably wouldn't have sought it. After all, a third Clinton terms more or less means he's going to die in office. Though to be fair, I'm not sure if Clinton and his advisers knew how bad his heart health was until he was forced to undergo surgery, which of course, was after the time when a "Clinton/Gore 2000" race would have taken place.
As to Bush v. Obama I think the answer is obvious. Obama wins in an even bigger landslide. However, I wonder if running against President Bush in the middle of the crisis means Obama has to adopt a more oppositional attitude towards the Bush administration's efforts in dealing with that crisis, simply to differentiate himself from Bush. Even without the 22, Bush in 2008 is pretty unlikely, for the same reason Truman 1952 is unlikely. Bush doesn't strike me as the type to run when his numbers are so low. Sure, Rove might be able to bring it up, but there's absolutely no way Bush wins.