The music, for one thing, is ridiculously catchy. It's well arranged and has great harmonies, counter melodies, the whole works. Also, did anyone else know Nathan Fillion could sing? I didn't. The other singers are really good--both Neil Harris and Felicia Day have the perfect voices for their characters.
The characters! Again Whedon does an awesome job with characterization. I felt like I really, really got to know everyone deeply, from Dr. Horrible himself to Captain Hammer.
And the plot! Whedon had me caught from the very first second to the final forty-second minute. I can't say anything without ruining the show, but really, it's great work by Joss yet again.
But why are you still reading this? Go watch it, now! It's only 42 minutes long. And it's excellent.