Here are some things I think are pretty obvious, but people are still missing them.

This might be pretty long, if I can remember all of it. So bare with me.

1. Penny does feel strongly for Billy, possibly more strongly than towards Captain Hammer. I think the major point in that is during So They Say, when Penny is singing her bit on the washer and dryer. Many people noticed that she had another frozen yogurt, presumably for Billy. She also looks towards the door when a man walks in; it is obvious she is waiting for him. But that's not most important part. I think the most important part is the lyrics, which people often overlook. I think that during her segment, when she is sitting on the drier and waiting/looking for Billy, she is also singing about him. I think when she sings “Should I stop pretending?” she is actually singing about her relationship with Billy, and that she should really stop pretending they are just friends, and start acknowledging that they have a much stronger relationship. In fact, she might have done just that if Billy actually showed up instead of plotting against Captain Hammer.

2. Another thing I noticed: Captain Hammer gives Dr. Horrible the finger during his finale “WAAAAY!” Awesome.

3. The ending. Oh dear, the ending. And I mean the last two seconds, “A thing…” Here's what I think it means. I do *not* think the whole thing was a dream. It happened. Here, what I think is the most important line in the whole show besides “The hammer is my penis”:

Penny: “Sometimes people are layered like that. There's something completely different underneath than what's on the surface.”

Billy: “And sometimes there a third, even deeper layer, and that one is the same as the top, surface one. Like with pie.”

As many people have figured out, Billy is Pie. On the outside he's Billy, lovelorn after Penny. On the second layer he's Dr. Horrible. On the third layer we have Billy again. When Penny dies, so does the first Billy layer, exposing the middle Dr. Horrible layer. However, there is still a Billy layer deep beneath, and he is not feeling a thing. It's hard to explain; you just have to understand it. The deepest Billy layer is small and numb by the end of the show, drowning in sorrow. I think you can see that during the scene when he's robbing the bank (during the montage at the end, during “everything you ever”, and he's giving looks like he just really doesn't care.

That's it for now, until I remember more.