I agree with you that the real feminist argument about Penny was that she was just there to be the (extremely tepid) love interest. Though she didn't bother me so much because she actually seemed to be Josh's deliberate parody of one of his own character types--Anne/Lilly/whatever-her-name ended up being, the former goth chick from Buffy who ended up running the homeless shelter in Angel, though much more spineless? In fact, I almost saw Penny as a deliberate sendup of the helpless self-sacrificing heroine role, *especially* with the headlines afterward ("Heroes Girlfriend Dead," "Whats-her-Name Killed by Horrible"), showing how absurd it was just as Captain Hammer was a beautiful parody of a superhero and Dr Horrible was a remarkable send-up not only of mad scientists in general but specifically of the evil Trio from Buffy.

OMG, typing that I just remembered that I thought the absolute funniest bits were Captain Hammer explicitly stating that yes, by his hammer he meant his penis, and also explicitly saying he'd had sex with Penny when receiving that award.