In the first episode with Roger, the audience was left to believe that Doof's dislike of him was from his "do-gooderness" but as the flashbacks continue, we realize what an evil little brother he really was. Poor Doof.
You somehow mixed two things I hold nearest and dearest to my heart: the greatest animated show currently airing, and the greatest internet video musical thing ever. I never even made the connection between Dr. Doofenshmirtz and Dr. Horrible, probably because Doof is evil on purpose. Anyway, awes...
I would feel so silly doing this, but it all comes together in the end.