Bill Donohue - Of course the eye catching element is Donohue compares Obama to former KKK leader David Duke. Although this is headline catching, shocking, and probably works on some level, this is also a fallacy of composition. The bishop comparing Obama to David Duke is like comparing someone with different values to a serial killer: you may disagree with someone else's values but that doesn't make them a monster. Additionally, the David Duke point makes it look like 1/2 of the country that agrees with Obama are all members of a white supremacist terrorist organization. Its a false dilemma that you are either with Bill or with the terrorists.
Additionally, partial birth abortion is a non-issue as it makes up 0.2 percent of the 1.3 million abortions (source). It is therefore comparable to Obama's recent efforts to cut the federal budget by only 17 billion dollars, which would cut the overall budget by much less than 1% --- its a purely a symbolic act or effort at placation.
Robert Boston - Fundamentally misunderstands the point of the debate; he's trying to keep a lid on what he sees as a manufactured controversy by saying it isn't currently an issue and therefore shouldn't become one (the is-ought problem). He suggests that this isn't news because the majority of Catholics don't care nor agree with the bishop and therefore Bill isn't a representative of anyone. Fox New's website asks and answers its own question with its headline "Fabricated controversy or real debate?" Unfortunately, the real heart of the issue is whether a minority opinion here should be important (resisting a Bandwagon fallacy).
Also, he uses the term "you people" which is pretty close to an ad hominem that hurts his own credibility, not Donohue's.
"Moderator" Megyn Kelly (thanks Kimberly) - Failed the hardest by only attacking Boston, and using bad arguments to do so.
Kelly: "I just want to challenge you on your point ... the claim that the catholic church has allowed all these people to speak -- pro death penalty and so on and so forth."Both the moderator and Boston failed to do their homework: George W. Bush gave the commencement and was given an honorary degree in 2001 after overseeing the execution of 155 people in Texas. There was no controversy at all about him coming despite this conflict with with Catholic dogma. It may be true that the death penalty is LESS bad than abortion, but no one made that point or tried to.
2009-05-19 edit: I formerly wrote that George W. Bush merely spoke at the college, but he in fact got an honorary degree.