I've heard feminist grumblings about Doctor Horrible's Sing-Along Blog since it came out. It
is a bit of a puzzle: Whedon is an explicitly feminist writer, so why is the female lead:
- the love interest of both male leads
- turned into a prize in the men's contest of Hero vs. Villain
- reduced to a trophy girlfriend at the shelter opening, an achievement she was responsible for
- killed as part of Dr. Horrible's origin story, a classic Women In Refrigerators scenario?*
I'm a fan of Whedonia in general, so I feel called upon to... well, not reflexively defend it, necessarily, but at least give it some good hard thinking through. Ultimately, I think it
is a feminist work--in that Penny's death could easily have been avoided if either man had made the slightest effort to treat her as something other than a prize in their hero vs. villain contest--but that, in a work as pared-down as this one, anything not central to the show's main themes doesn't get any emphasis. Feminism, in this work, being peripheral to the main points--which, I think, are mostly about black-and-white duality and its traps--it falls by the wayside.
For the three of you who've never seen DHSAB, the world sketched out in the 45-minute film follows familiar enough contours: Los Angeles is threatened by supervillains and defended by superheroes, while regular people read about it in the papers and try to stay out of the way. But designated superhero Captain Hammer is... well, a dick; mostly interested in his own self-image and squashing anyone whose views differ from his, more devoted to the idea of protecting and helping people than to actually doing so, seemingly incapable of interacting with a woman without hitting on her.
His opponent, to balance the scales, is curiously sympathetic. Doctor Horrible is smart and alienated and punctilious, for a supervillain: of course he wants to rule the world, but he plays by the rules in the meantime.
Enter local do-gooder Penny, with a third way--the notion that people can solve their own problems without waiting for the supers, and the willingness to accept the world as it is rather than as she thinks it should be. At times she's positively taoist:
Penny: Everything happens--
Billy: Please don't say "for a reason".
Penny: No, I'm just saying... Everything happens.
Penny is the wisest and most mature of the three leads, and the only one comfortable with duality:
Penny: Even in the darkness, every color can be found / And every drop of rain brings water flowing to seeds growing in the ground
Maybe that's why she accepts being overshadowed by Captain Hammer: she knows that her cause is bigger than she is, and, unlike either man (especially Dr. Horrible), she is willing to seek and accept help. She may not have realized the extent to which Captain Hammer would seize the credit--her awkwardness at the shelter opening suggests that she does not--but that's not Penny's fault so much as it is Captain Hammer's and, especially, the ordinary people (the movers, the newscasters, etc.) who give Hammer the credit because they expect superheroes to solve their problems.
Mover 1: So they say Captain Hammer's become a crusader, political; he's cleaning up the town
Mover 2: 'Bout time!
and
Both news anchors: It's the perfect story
Anchorman: So they say
Anchorwoman: A hero leading the way
Both: Hammer's call to glory...
In other words, that Penny's work was co-opted by Captain Hammer seems to be less because she's a woman and more because she's not a superhero.
*Note, also, that DHSAB fails the Bechdel Test.
was nominated once before, for the utterly brilliant Buffy the Vampire Slayer episode, "Hush." (The brilliance of that episode lies in its back-handed petulance -- everyone went on about how wonderful Mr. Whedon's dialogue was, and so he wrote a brilliant episode in which no one can speak after the first few minutes.) 
I could go on about how the new, sparkly take on the vampire myth has transformed one of our culture's most enduring and evocative monsters into a 
