So far I haven't run into much actual critique of the whole movie. So:

I liked that it was
stretched over a few days. I was lulled into a false sense of security
over the goofy, light-hearted nature of the story, and rather than
maintaining it for 40 minutes before I'm surprised, I maintained it for
a good few days. The longer you believe something, the more you
believe it, and I was thrown by the ending more than I would have been
had I seen all three parts for the first time at once.

I
liked the duets between Neil Patrick Harris and Felicia Day (especially
the one from the beginning of Act 2). I hope they do something musical
together again, because their voices blend beautifully.

The use of rather goofy humor mixed in with the deathly serious bits was great. It keeps the scene from getting too bogged down by a “woe is me” tone and it screws with the viewer's head.

And
I liked the use of the goggles. They were an important part of the
costume, but if Dr. Horrible had worn them on his face, it would have
made him totally unexpressive, so that was saved for his full
conversion to badass evil Dr. Horrible. It even added to the
conversion, as the drop in expression caused his face to appear less
feeling, less human. Besides that, they reminded me of Razputin from
Psychonauts (and Psychonauts is awesome).

What I didn't like:

The
timing in Act 1 was really slow. I keep trying to get people to watch
Dr. Horrible, but half of them get bored and turn it off because the
beginning takes so long to get going.

The background instrumentals were flat and unimpressive in most of the songs. I understand that a tight budget makes instrumental music awkward, but they had rich enough instrumentals in a few songs (the last song of Act 2 and the last song of Act 3 especially), so why not in all of them? Just because you're not rocking out doesn't mean you can't have a solid instrumental part.

There was a lack of Star Wars references. Everything cool is supposed to have a Star Wars reference somewhere, and I guess it's possible that I missed it, but I don't think Dr. Horrible had one. So get on that.

Oh, myyyyyyyyyyyyy! I got the Star Wars reference alright!

Or maybe I am twisted…

Everyone has been talking about the end, it´s like the start of a supervillain (the counterpart of a superhero start like in Batman returns…).

Well, how about the end of episode 3? Isn´t it the start of a supervillain that did everything to save his love and in the meantime she accidentally dies? And the googles? Well, that´s like the hideous black helmet of Vader, right?

There is your subtle reference. (Well so subtle that I think I just made it up).

Only Whedon did it way better, and more credible and more tragic.

If only Whedon had directed the prequels…