"Another One Rides the Bus" - I love AORTB, partially because it's so musically different than the original. That said, I do miss the groove sometimes. I have a feeling the early songs will come up frequently in this topic.
"She Drives Me Crazy" - I know Al said he was going for a cartoony voice since Roland Gift's is so hard to duplicate...but I really don't like the vocal here. It's too over-the-top on the choruses and hard to understand during the verses. Plus, I don't really feel that the joke progresses any; it's pretty one-note...although I love the hitchhikers line.
"Bohemian Polka" - Yeah, it's not a parody, but still.
"Misery" - I don't think anyone will really argue this one.
I won't get into unreleased songs here, but "Pacman" definitely would make the list.
Then there are some where I enjoy both versions about equally: "Beat It," "Smells Like Teen Spirit," "Rico Suave" (shut up!), "eBay" (shut up again!)
All in all, Al has a pretty awesome track record.
