anything where penny and horrible were happy in the end, and hammer was exposed as he really is.

or more realistically- horrible's plan failing without anyone but him knowing, penny leaving hammer and getting with billy and billy never having to be horrible again. Plus that way hammer is left lonely and stupid. tee hee

While at work and letting the songs running through my mind, I was struck by the line from the end of Act I, where Captain Hammer sings (twice) "Seems destiny ends with me saving you".

Knowing how musicals love to reprise songs, it occured to me those words could come from Horrible's mouth: he has to abandon his plans to kill Captain Hammer to rescue her.

Penny seemed a bit … [i]obsessed[/i] with changing people's lives for the better. It had occurred to me, therefore, that she might have been aware that Billy was actually Dr Horrible all along, and was trying to guide him into a better life.
This could combine with the reprise above. A "reformed" Dr.Horrible, bent on being a genuine hero (rather than a glory hound/bully like Captain Hammer) could fit into Penny's life quite well.

But now I can see that wasn't the direction this was going in. The foreshadowing is obvious, in retrospect.

As much as I was dying to see Captain Hammer get splattered as Dr Horrible raised his death ray (ok, so he doesn't deserve to die, but he was still a jerk and that song totally psyched me up)…however, I wouldn't like any other ending than the one that was there. Artistic vision ftw.

That said, damn you Joss Whedon for making me care about your characters so much.