My favorite lines are:

Oh goodnees, look at my wrist! I gotta go.

My penis is the hammer.

"The hammer is my penis"

There were a lot of great lines but these were my favorites:
"What a crazy random happenstance!"

"Trust your instincts"

"I say succsesful in that I archieved my objective it was less succesfull in that I inadvertently introduced my arch nemesis to te girl of my dreams"

"Peace but not literaly"

"a shiny new Australia"

"I mean, if you're gonna get into the Evil League of Evil, you have to have a memorable laugh. What, do you think Bad Horse didn't work on his whinny? His terrible death-whinny?"

"The Hammer is my penis."

"Oh goodnees, look at my wrist! I gotta go"

"And sometimes there's a third, even deeper level, that one is the same as the top suffice one. Like with pie."

"smoother an old lady""Do I even know you?"

I LOVE the hammer one!!! And the pie one!!! Oh and this one too!

"The world is a mess, and I just need to rule it."

=D

Love the hammer line, and crazy random happenstance too.

Also love "...someone like Bad Horse." "The thoroughbred of sin!?!"

"These are not the hammer, the hammer is my penis."

"It's curtains for you, Dr. Horrible- lacey, gently wafting curtains."

"Wow, sarcasm. That's original."

"Destroying the status quo, because the status is NOT quo. The world is a mess and I just need to rule it."

"I also need to be a little bit more careful about what I say on this blog, apparently the LAPD and Captain Hammer are among our viewers."

So many good lines to choose from!

Lol so many good QUOTABLE lines to choose from! Gosh Dr. Horrible is love now!!

fanfly those are my favorite quotes too. :) dr. horrible is absolutely fantastic.

"Dude, you are not my nemesis."

"Balls."

"I just might sleep with the same girl twice. I hear it's better the second time. I hear they like to do the weird stuff."

"We have a problem with her."

"We totally had sex."

and most of the above quotes.

I agree with shieldmaiden.

I'm with Candi...my favorite line is Captain Hammer's line from the "Perfect Day" Song:

"This is so nice. I just might sleep with the same girl twice. They say it's better the second time. They say you get to do the weird stuff."
[groupies: "We do the weird stuff!"]

Oh and how could I forget...
"You got a little crush, don't you Doc? Well that's gonna make this hard to hear. See, later I'm gonna take little Penny back to my place, show her the Command Center, Hammer Cycle, maybe even the Ham-Jet. You think she likes me now? I'm gonna give Penny the night of her life. Just because you want her, and I get what you want. See, Penny's giving it up. She's givin it up hard, cause she's with Captain Hammer. and THESE are not the hammer."

And I've omitted the other great line at the end of this that's already been mentioned :-)

"I want to be an achiever. Like Bad Horse."
"The thoroughbred of sin?"
"I meant Gandhi."

Penny: "what about your clothes?"
Billy: "I don't love these!"

Moist: "Do you need anything dampened, or made soggy?" (I find that line hilarious and i don't know why). :-p

THose are all really good lines.
It is so hard to choose from any of them.

-"but what about your clothes?"
"...I don't love these!"

-"I want to be an achiever... like Bad Horse."
"The thoroughbred of sin??"
"...I meant Gandhi."

-"So did you spend all weekend hunting wild signatures?"
"no, actually I went on a date."
"...get right outta town! how was that?"

"And sometimes there's a third, even deeper level, that one is the same as the top one.
"...what?"
"Like with pie. So you going to see him again?"

god... I could go on, but let's just say I like nearly every line in Dr. Horrible and Penny's conversation about Captain Hammer. Dr. Horrible is so hilarious with just slipping in the little side comments like "trust your instincts."

obviously, there are about 300,000,000,000 more... but I don't really need to go on about it. xD

"I don't have time for every poser in a parka."

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"Plus, there are KIDS in that park, sooo..."
absolute favorite line in the show, I don't know why I like it so much... XD

"Captain Hammer threw a car at my head"
Not a funny quote, but I love the way Neil delivered the line.

I luv ALL the quotes from above.
"Moist! My evil...moisture buddy."
"This world is going to BURN! BURN! Yeah, that´s two rrs. H-o-r-r-yeah, that´s right. BURN!!"
Or the part where Billy was talking about cutting the head off the human race. That was hilarious, especially Penny´s reaction.
"Love your hair." "What?" "No, I love the-the air!"

"Oh my goodness, look at my wrist, i gotta go!" XD

And,

Penny: "Hey, I know you."
Billy: "Hello. You know me, cool. I mean, yeah, you do...Do you?"

and also

Penny: "Will you lend a caring-"
Billy: Ah, ahh, ahh, ahh... What?!"

XD "My theory is to cut off the head!" "Of the human race?"

"Love your hair."

"What?"

"N-no I.. I love the.. the air.. heh..."

"Society is slipping. Everything is slipping, awaaay!"

'balls" ,"SMOTHER AN OLD LADY!" "do i even know you?" xD