Transcribed all the Act III lyrics, though some of it's still a little questionable. Cleaned up the ones from Act I and Act II from http://imaekgaemz.com/?page_id=52.

Update: I keep tweaking this. Thanks to everyone who commented with corrections, even if it took me awhile to weed my way through comment spam to find them. (Is that Wil on 7/22, The Wil? The one dancing barefoot?)

Dr. Horrible's Sing-Along Blog - Act I

Freeze Ray (Billy)

Laundry day
See you there
Underthings
Tumbling.

Wanna say,
"Love your hair."
Here I go,
Mumbling.

With my freeze ray
I will stop the world.
With my freeze ray
I will find the time to
Find the words to

Tell you how
How you make
Make me feel
What’s the phrase?

Like a fool
Kinda sick
Special needs
Anyways

With my freeze ray
I will stop the pain.
It’s not a death ray
Or an ice beam

That’s all Johnny Snow.
I just think you need time to know

That I’m the guy to make it real
The feelings you don’t dare to feel
I’ll bend the world to our will
And we’ll make time stand still

That’s the plan
Rule the world
You and me
Any day

Love your hair
PENNY (spoken): What?
BILLY (spoken): No I... I, I… I love the air
Anyway

With my freeze ray
I will stop–

The Application (Bad Horse Chorus)

BAD HORSE CHORUS #1: Bad Horse
BAD HORSE CHORUS #3: Bad Horse
BAD HORSE CHORUS: Bad Horse
Bad Horse

He rides across the nation,
The Thoroughbred of Sin.
He got the application
That you just sent in.

It needs evaluation,
So let the games begin.
A heinous crime, a show of force
A murder would be nice of course.

Bad Horse
Bad Horse
Bad Horse
He’s Bad

The Evil League of Evil
Is watching, so beware.
The grade that you receive
Will be your last we swear,
So make the Bad Horse gleeful,
Or he’ll make you his mare.

Get saddled up.
There’s no recourse.
BAD HORSE CHORUS #3: It’s Hi-Ho Silver!
BAD HORSE CHORUS: Signed, Bad Horse

Caring Hand (Penny)

Will you lend a caring hand
To shelter those who need it.
Only have to sign your name
Don’t even have to read it.

Would you help?
No?
How about you?

A Man's Gotta Do What a Man's Gotta Do (Billy/Dr. Horrible, Captain Hammer, Penny)

BILLY:
A man’s gotta do what a man’s gotta do.
Don’t plan the plan if you can’t follow through.
DR. HORRIBLE:
All that matters, taking matters into your own hands.
Soon I’ll control everything, my wish is your command.

CAPTAIN HAMMER:
Stand back, everyone, nothin' here to see.
Just imminent danger, in the middle of it, me.
Yes, Captain Hammer’s here, hair blowing in the breeze.
The day needs my saving expertise.

A man’s gotta do what a man’s gotta do.
It seems destiny ends with me saving you.
The only doom that’s looming is you loving me to death.
I’ll give you a sec to catch your breath.

DR. HORRIBLE (spoken): You idiot!
CAPTAIN HAMMER (spoken): Dr. Horrible. I should have known you were behind this.
DR. HORRIBLE (spoken): You almost killed her.
CAPTAIN HAMMER (spoken): I remember it differently.
DR. HORRIBLE (spoken): If she-
CAPTAIN HAMMER (spoken): It's curtains for you, Dr. Horrible. Lacy, gently wafting curtains.
DR. HORRIBLE (gurgled): ?

PENNY:
Thank you, Hammer-Man, I don’t think I can
Explain how important it was that you stopped the van.
I would be splattered, I’d be crushed into debris.
Thank you, sir, for saving me.

(in harmony)
CAPTAIN HAMMER: Don’t worry about it-a man’s gotta do what a man’s gotta do.
PENNY: You came from above.
DR. HORRIBLE: Are you kidding?

CAPTAIN HAMMER: It seems destiny ends with me saving you.
DR. HORRIBLE: What heist were you watching?
PENNY: I wonder what you’re Captain of.
DR. HORRIBLE: Stop looking at her like that!

CAPTAIN HAMMER: When you’re the best, you can’t rest, what’s the use?
DR. HORRIBLE: Did you notice that he threw you in the garbage?
PENNY: My heart is beating like a drum.

CAPTAIN HAMMER: If there’s ass needs kicking, some ticking bomb to defuse.
DR. HORRIBLE: I stopped the van… The remote control was in my hand.
PENNY: Must…. Must be in shock

CAPTAIN HAMMER: The only doom that’s looming is you loving me to death.
PENNY: Assuming I’m not loving you to death.
DR. HORRIBLE: Whatever.

CAPTAIN HAMMER: So please give me a sec to catch my breath.
PENNY: Please give me a sec to catch my breath.
DR. HORRIBLE: Balls.

Dr. Horrible's Sing-Along Blog - Act II

On the Rise (Billy, Penny)

BILLY:
Any dolt with half a brain
Can see that humankind has gone insane
To the point where I don’t know If I’ll upset the status quo
If I throw poison in the water main.

Listen close to everybody’s heart
And hear that breaking sound.
Hopes and dreams are shattering apart
And crashing to the ground.

I cannot believe my eyes,
How the world’s filled with filth and lies,
But it’s plain to see evil inside of me
Is on the rise.

PENNY:
Look around.
We’re living with the lost and found.
Just when you feel you’ve almost drowned,
You find yourself on solid ground.

And you believe there’s good in everybody’s heart.
Keep it safe and sound.
With hope, you can do your part
To turn a life around.

I cannot believe my eyes.
Is the world finally growing wise?
Because it seems to me some kind of harmony
Is on the rise.

(in harmony)
BILLY: Anyone with half a brain
PENNY: Take it slow.

BILLY: Could spend their whole life howling in pain,
PENNY: He looks at me and seems to know

BILLY: Because the dark is everywhere and Penny doesn't seem to care
PENNY: The things that I’m afraid to show

BILLY: That soon the dark in me is all that will remain.
PENNY: And suddenly I feel this glow.

BILLY: Listen close to everybody’s heart
PENNY: And I believe there’s good in everyone’s heart.

BILLY: And hear that breaking sound.
PENNY: Keep it safe and sound.

BILLY: Hopes and dreams are shattering apart
PENNY: With hope, you can do your part

BILLY: And crashing to the ground.
PENNY: To turn a life around.

BILLY: I cannot believe my eyes
PENNY: I cannot believe my eyes

BILLY: How the world’s filled with filth and lies
PENNY: How the world’s finally growing wise

BILLY: But it’s plain to see evil inside of me
PENNY: And it’s plain to see rapture inside of me

BILLY: Is on the rise
PENNY: Is on the rise

Assassination (Bad Horse Chorus)

He saw the operation
You tried to pull today,
But your humiliation
Means he still votes “Nay”.
And now assassination
Is just the only way.

There will be blood.
It might be yours,
So go kill someone.
Signed, Bad Horse.

Keep Your Head Up (Penny)

Here’s a story of a girl
Who grew up lost and lonely,
Thinking love was fairy tale,
And trouble was made only
For me.

Even in the darkness
Every color can be found,
And every day of rain brings water
Flowing to things growing in the ground

Grief replaced with pity
For a city barely coping.
Dreams are easy to achieve,
If hope is all I’m hoping
To be

Anytime you’re hurt
There’s one who has it worse around,
And every drop of rain will keep you
Growing seeds you’re sowing in the ground.

So keep your head up, Billy-Buddy.

Brand New Day (Billy/Dr. Horrible)

BILLY:
This appeared as a moral dilemma cause at first
It was weird though I swore to eliminate the worst
Of the plague that devoured humanity it’s true
I was vague on the "how," so how can it be that you
Have shown me the light?

It’s a brand new day,
And the sun is high.
All the birds are singing
That you’re gonna die.
How I hesitated
Now I wonder why.
It’s a brand new day.

DR. HORRIBLE:
All the times that you beat me unconscious I’ll forgive
All the crimes incomplete, listen, honestly I’ll live.
Mr. Cool, Mr. Right, Mr. Know-it-all Is through,
Now my future’s so bright, and I owe it all to you,
Who showed me the light.

It’s a brand new me.
I’ve got no remorse.
Now the water’s rising,
But I know the course.
I’m gonna shock the world.
Gonna show Bad Horse
It’s a Brand New Day.

And Penny will see the evil me.
Not a joke, not a dork, not a failure.
And she may cry, but her tears will dry,
When I hand her the keys to a shiny new Australia.

It’s a brand new day.
Yeah, the sun is high.
All the angels sing,
Because you’re gonna die.

Go ahead and laugh.
Yeah, I’m a funny guy.
Tell everyone goodbye.
It’s a brand new day.

Dr. Horrible's Sing-Along Blog - Act III

So They Say (Ensemble)

MOVING GUY:
So they say Captain Hammer's become a crusader
Political. He's cleaning up the streets.
OTHER MOVING GUY (spoken): About time!

GROUPIE #1: So they say that it's real love.
GROUPIES: So romantic!
GROUPIE #2: He signed this.

PENNY:
So they say we'll have blankets and beds.
We can open by monday, thanks to you.
CAPTAIN HAMMER: Thanks to me.

NEWSMAN and NEWSWOMAN: It's the perfect story.
NEWSMAN: So they say.
NEWSWOMAN: A hero leading the way.
NEWSMAN and NEWSWOMAN : Hammer's call to glory.
NEWSWOMAN: Let's all be our best.
NEWSMAN: Next up, who's gay?

GROUPIE #3: So they say he saved her life.
GROUPIE #1: They say she works with the homeless and doesn't eat meat.
GROUPIE #1: We have a-
GROUPIES: -problem with her.
GROUPIE #2: This is his hair.

CAPTAIN HAMMER:
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!

PENNY:
This is perfect for me, so they say.
I guess he's pretty okay
After years of stormy sailing
Have I've finally found the bay?

MOIST (spoken): He's still not picking up

PENNY and DR. HORRIBLE: There's no happy ending, so they say.
DR. HORRIBLE: Not for me anyway
PENNY and DR. HORRIBLE: Should I stop pretending

DR. HORRIBLE: Take the chance to build a brand new day
PENNY: That this is a brand new day.

GROUPIE #2: This is a dry cleaning bill.
GROUPIES: Four sweater vests!

Everyone's a Hero / Slipping (Captain Hammer, Dr. Horrible)

CAPTAIN HAMMER:
It may not feel too classy
Begging just to eat,
But you know who does that? Lassie,
But she always gets a treat.

So you wonder what your part is,
'Cause you're homeless and depressed,
But home is where your heart is,
So your real home's in your chest.

Everyone's a hero in their own way.
Everyone's got villains they must face.
They're not as cool as mine,
But folks you know it's fine
To know your place.

Everyone's a hero in their own way,
In their own not-that-heroic way.

So I thank my girlfriend, Penny.
Yeah, we totally had sex
She showed me there's so many
Different muscles i can flex.

There's the deltoids of compassion.
There's the abs of being kind.
It's not enough to bash in heads,
You've got to bash in minds.

Everyone's a hero in their own way.
Everyone's got something they can do
Get up, go out and fly
Especially that guy
That smells like poo.

Everyone's a hero in their own way.
You and you and mostly me and you.

I'm poverty's new sheriff,
And I'm bashing in the slums.
A hero doesn't care if you're
A bunch of scary alcoholic bums.

(spoken) Everybody!

Everyone's a hero in their own way.
Everyone can blaze a hero's trail.
Don't worry if it's hard.
If you're not a frggin' tard
You will prevail!

Everyone's a hero in their own way.
Everyone's a hero in their own-

DR. HORRIBLE:
Look at these people.
Amazing how sheep'll
Show up for the slaughter.
No one condemning
You lined up like lemmings
You led to the water.

Why can't they see what I see
Why can't they hear the lies
Maybe the fee's to pricey
For them to realize
Your disguise is slipping.
I think you're slipping.

Now that your saviour
Is as still as your grave you're
Beginning to fear me
Like cavemen fear thunder
I still have to wonder
Can you really hear me?

I bring you pain
The kind you can't suffer quietly.
Fire up your brain
Remind you inside your rioting society
Is slipping
Everything's slipping away

So,

Go ahead, run away!
Say it was Horrible.
Spread the word, tell a friend.
Tell them the tale.

Get a pic. Do a blog.
Heroes are over with.
Look at him. Not a word.
Hammer meet nail!

Then i win, then I get
Everything I ever
All the cash, all the fame
And social change.

Anarchy, then i run.
It's Dr. Horrible's turn.
You people all have to learn
This world is going to burn!
Burn!
(spoken) Yeah, it's two r's, H-O-R-R, yeah, right.
Burn!

No sign of Penny.
Good, I would give anything
Not to have her see.
It's gonna be bloody.
Head up, Billy-Buddy.
There's no time for mercy.

Here goes no mercy!

(spoken) That's not a good sound.

CAPTAIN HAMMER:
-Waaaaaaaaay!

Dr. Horrible Is Here (Billy/Dr. Horrible)

DR. HORRIBLE:
Here lies everything
The world I wanted at my feet
My victory is complete
So hail to the king
(Everything you ever)
Arise and sing

So your world's benign
So you think justice has a voice
And we all have a choice
Now your world is mine
(Everything you ever)
And I am fine

Now the nightmare's real.
Now Dr. Horrible is here
To make you quake with fear,
To make the whole world kneel.
(Everything you ever)
And i won't feel-

BILLY:
-a thing.