Well, the stock answer would be "good triumphs over evil". IE, Captain Hammer defeats Dr. Horrible's plan, Dr. Horrible ends up in prison, and Penny and Captain Hammer get married.
Yuk. And, it isn't going to happen. Dr. Horrible is our protagonist, and our sympathies lie with him. Captain Hammer is pretty much a jerk. Penny is obviously clueless but seems to have some feelings for Dr. Horrible.
We could have the opposite, where Dr. Horrible kills Captain Hammer, wreaks havoc, gets into the League, and gets Penny.
There's the all-happy ending. Dr. Horrible sees the error of his ways, becomes good, and teams up with Captain Hammer to fight crime. Penny ends up with Dr. Horrible long-term after the thing with Captain Hammer goes sour. Perhaps even Penny's love turns Dr. Horrible into good.
I doubt either of these, too. There will be no killing in "Dr. Horrible" and any victory will, while still being a victory, will be minor in the big scheme of things. Dr. Horrible will remain evil, to some degree of evil.
Most likely, Dr. Horrible's plan to kill Captain Hammer will fail but Captain Hammer will be revealed to be a big a-hole and suffer a huge embarassment. Penny will realize Dr. Horrible is the one for her. Dr. Horrible gets into the League of Evil, Captain Hammer slinks away, and there's a kind-of happy every after ending.
One thing that would be fun would be if Penny was actually evil, and perhaps was getting the building not for the homeless shelter but for furthering her evil cause. She did recognize who "Bad Horse" was, very quickly.
It would also be nice if Moist played a part in helping Dr. Horrible get what he wants.
And now, off to watch the show. If there's time. I have to leave for the play in an hour. We'll see how I did.