It's always dangerous when you read into stuff that isn't there… especially in comic-bookish style entertainment. Warning aside, I started wondering about Penny's "death."
For all intents and purposes, Penny suffered a shrapnel wound. The first rule of shrapnel injury is NOT to remove the shrapnel at the scene. It's likely to be hot and the site should be irrigated. However, after she "dies", we see Dr. Horrible lift Penny onto a gurney with the Shrapnel missing. I recognize the possibility of surviving those wounds are marginal at best, there may have been significant internal bleeding, and that the medics didn't seem to concerned about transporting her out of the site in any haste, but I can't help but wonder a few things:
1. The external bleeding was fairly minimal for a puncture wound. Even after the removal of the shrapnel, there just isn't much for blood. I've seen bloody noses that are far more intimidating. I guess you could say that Dr. Horrible removed the shrapnel after she died and that before she died it was just an issue of parts sealing the site.
2. What if Penny's death wasn't a death? What if she had just lost consciousness from blood loss? Granted we didn't see much external blood loss, but it could have been internal injuries.
3. What if she DID die but it was partially a result of Dr. Horrible's mis-care (early removal of the shrapnel)?
4. After Penny's death, things sort of got "surreal" and there were reporters asking why Dr. Horrible killed [Penny]. However, it wasn't the first time that Dr. Horrible's imagination took over. In "A Brand New Day" he fantasizes about squishing Captain Hammer and in the early part of the song, he sort of sings to Captain Hammer. At no point do we believe he's actually in Hammer's face telling him that the birds are singing that he's "…gunna die!" We have to realize that his imagination is not without precedence in this universe.
Now, if in part four we find out she didn't die, it will "happy things up", but I think it will take a lot of the meaning away from Dr. Horrible. I think Whedon struggles with the balance and the bitter/sweetness. It's hard to have a true scale of beauty if you don't have some contrasting ugliness. I also want to echo another poster in these forums who stated that if there is never any real threat to main characters, there is no suspense and no real reason to fear a situation (paraphrasing). However, I'm just getting at the fact that this doesn't necessarily have to be the end of Penny. There is enough inconsistency to say that the door isn’t completely shut on her.
As nasty as this sounds, I'd prefer to allow Penny's death to color Dr. Horrible and have him learn to live with that tragedy. Perhaps his memory of her will resurrect "Billy" and help him to take the path he failed to take before. There are lots of ways to play this. I just wanted to point out that Penny isn't necessarily "dead."