I like 2 and 3. Perhaps consider taking a drink every time Penny is on screen and she's not paying any attention to Dr. Horrible. He's constantly ignored and there's something to that.
I'm a bit late to the party, but at my college, my group of friends have been doing what we call 'Dr. Horrible's Drink along Blog' for about 2 years now. The rules are as follows...
1.Anytime a song Starts 2.Anytime Dr. Horrible twitches his eye 3.Anytime Captain Hammer is Overly Douchy or cheesy 4.Anytime Penny is overly Uplifting 5.Anytime Dr. Horrible/Billy is Emo 6.Anytime there is a Pun.
We also all pick our favorite line and everyone drinks to those, and just end up drinking at whatever makes us laugh. I'm pretty sure your thing is over now, but just in case you ever want to have one again! Hope it was fun!