Has anyone else been wondering about the beginning of that song? 

"Here lies everything, the world I wanted at my feet"

To me, it seems like that has two meanings: he has the world at his feet (he is in charge now) because he accomplished what Bad Horse wanted (killing someone) and he can now be in the ELE… sort of victorious sounding, definitely the Dr. Horrible interpretation. Then there's Billy, and (while I'm not saying Billy is a separate personality, just another aspect) he really just wanted Penny. She represented the world he wanted (or was the world he wanted) and now is lying at his feet, literally. Dead, of course. Incredibly sad.

I love how that single line not only has double meanings, but the meanings represent opposite ends of the emotional spectrum, and somehow the way NPH sings them you still couldn't say definitively whether it was one or the other.

In the classic view of most superheroes/supervillains, there's always a dual personality involved.  This is perhaps one of the better tellings of it I've ever seen or read.  As he's standing over the body of Penny, Dr. H is doing a gloating victory song, however in a very sad almost funereal sort of way.  In my mind, its 2 deaths – Penny just died and Billy is dying right there with her.  But as the song goes along, heading to the party scene, you are seeing him become more and more Dr. Horrible.  The kernel inside that once was Dr. Horrible is now the entire personality, leaving the smallest of spaces in him left to Billy.  At this point there's really nothing left of Billy, other than a pervasive sadness of what might have been.