Here are my favorites from City of Bones:
1) Jace: Your friend's poetry is terrible...It sounds like he ate a dictionary and started vomiting up words at random.
2) Clary:Those girls on the other side of the car are staring at you.
Jace: Of course they are. I am stunningly attractive."
Clary: Haven't you heard that modesty is an attractive trait?
Jace: Only from ugly people.
3) Clary thinking silently to Valentine: That sounds terrific. Just you and your comatose wife, your shell-shocked son, and your daughter who hates your guts....Yeah, that sounds like a perfect family reunion.
4) Clary: I figured all your classes were Slaughter 101 and Beheading for Beginners.
5) Clary: Well, there goes my plan for selling them (blades) on eBay.
Jace: Selling them on
what?
Clary: A mythical place of great magical power.
6) Simon: I thought it'd be something cooler, like a van with "Death to Demons" painted on the outside...
7) Simon: If this is your idea of glamour, I'm having second thoughts about letting you make me over.
8 ) Jace: I don't hate them (Silent Brothers). I'm afraid of them. It's not the same thing.
Simon: I thought they were librarians.
Luke: They are librarians.
Simon: Those must be some killer late fees.
9) Clary: Sarcasm is the refuge of the imaginatively bankrupt.
Jace: I can't help it. I use my rapier wit to hide my inner pain.
10) Madame Dorothea: Of course there's a parlour. Where else would I entertain?
Jace: I'll just leave my hat with the footman.
11) Isabelle: Maybe we should all have codenames.
Jace: Good idea. I shall be Hotschaft von Hugenstein.
12) Alec muttered a retort into his coffee. It rhymed with something that sounded a lot more like "ducking glass mole."
13) Jace: I wouldn't feel too sorry for him (Simon, as a rat). That's probably the closest he's ever gotten to second base.
Clary: Shut up.
14) Clary to Magnus: Simon's not dim-witted.
Jace: It's true. He just
looks dim-witted. Really, his intelligence is quite average.
15) Jace: He (Simon) has many things I haven't got. Like nearsightedness, bad posture, and an apalling lack of coordination.
16) Simon: Was it weird, hearing from Jace? I mean, since you found out...
Clary: Yes? Since I found out what? That he's a killer transvestite who molests cats?
Simon: No wonder that cat of his hates everyone.
Clary: Oh, shut up, Simon.
Of course, I also like the other quotes that everyone has posted.