Then there's the moment in "Wake the Devil" where Hellboy is fitted with the B.P.R.D.'s latest jetpack, assured that it's "new and improved," and then thrown out of a plane before he has a chance to argue. He subsequently clicks the button to activate the jetpack... and keeps clicking it as he falls, with zero results, until the final click, which causes the jetpack to explode.
"Now God has a tree in his neck." from Almost Colossus.
This little gem from Strange Places.
Hellboy: So you had a dream that when I die the whole world gets destroyed and you're going to prevent that— by killing me? You're a genius.
There's another bit from Strange Places where Hellboy comes across a golden lake by a castle.
Hellboy: Ah, screw it. *Steps into the water*
*Cue giant eel monster bursting out of the water*
The entirety of "Buster Oakley Gets His Wish", even the half-cow. But the best part is Hellboy's reaction to the attempt at Anal Probing.
In "Curse of the Haunted Dolly", Kate Corrigan accidentally unleashes a ghost of her recently-deceased mother, who keeps bugging her to have grandchildren. Cut to Kate at the cafeteria with Abe and Kraus. The following gem happens next.
Abe: So, how'd you get rid of her?
Kate: I told her I'd marry a doctor, move to the suburbs, and have a bunch of kids.
"I hate those comic books. They never get the eyes right."
Hellboy gets run over by a train, and the axles keep hitting his horn stubs. By the time the train is gone, the stubs are red-hot. And then he scorches his hand on them.
Hellboy. Payphone. "IT'S FOR YOU!!" (SMASH!)
In the same fight
Hellboy: Uh uh, second date, NO TONGUE!" *grabs demon's tongue and uses it to smash demon through a wall*
"Heh, heh. Nachos."
The whole scene on the rooftop when Hellboy stalks Liz and Myers, snarking every occasion he gets, only to freeze because Liz took Myers' picture.
He then proceeds to mutter this to himself repeatedly, apparently trying to give himself the determination to make the jump to the next building. He jumps, hangs in the air for a second, and then goes "Oh, crap!" as he realizes he's coming up short.
"...and you're nine. You shouldn't be giving me advice."
"What's a good, strong word for 'need'?" "Well, 'need' is a good, strong word." "Too needy."
Myers: I am not pure of heart! Abe: (interrupting) Yes you are.
Myers hands Hellboy a grenade belt. His response: "I didn't get you anything".
Manning has some quality snarking at the museum crime scene.
Abe: Professor! They were here.
Manning: Who was here? Nixon? Hoodini? Jimmy Hoffa? Who?
"Gonna be sore in the mornin'."
After the first Sammael attack, Hellboy and Myers hide behind a dumpster to reload the Samaritan. Hellboy then finds a huge disgusting detached thing on his arm from Sammael's tongue.
Myers: (clearly freaked out) What the hell is that thing?!
Hellboy: (calmly pries it off, pauses) Let me go ask. (hands it to Myers, who smacks it away in horror)
Right up until the soldiers see the Nazi soldiers at work on the island, the sergeant in charge is hugely skeptical of Professor Broom, claiming that there's nothing there except "sheep and rocks". The second they see what's really going on, he is shocked, and Broom's response is priceless.
BROOM: They must be here for the sheep.
Hellboy II: The Golden Army
The fight between Hellboy and Dr. Krauss. note Alternatively, Hellboy vs. Lockers. Lockers win.
Hellboy: Look, Kraut... Krauss: That's KRAUSS! With a double S! Hellboy: "SS"... riiighhhtt.
Another contender: "Can't Smile Without You". Without a doubt the greatest duet ever put to film, you're not even sure what you're supposed to do when they start singing in a Hellboy movie. Laugh? Cry? Run away? What?
Which the flick eventually elevates to "cool" status by re-including it in the credits, providing a sort of punchline for the movie itself.
Abe. Drunk. 'Nuff said.
When Hellboy first offers him a beer, Abe refuses with "My body's a temple." "Well now it's an amusement park" comes Hellboy's reply. The delivery of both lines is perfect.
Manning slowly losing his mind.
Hellboy punches out a goblin for trying to eat cats, the thing is that the goblin is currently disguised as an old lady and he knocks her right out of her orthopedic shoes.
The part where Manning is complaining about Hellboy being photographed, and the first few we see are the usual grainy "what is that red thing in the distance?" shots... then Manning goes, "He posed for this one!" holding up a photo with Hellboy giving a thumbs up and a goofy grin. And then he walks off muttering "God, I hate YouTube."
"I'm not a baby, I'm a tumor."
The part where, no thanks to Krauss's extra-thick accent, his pronunciation of "focus" made it sound like a dirty word.
Liz: I have a shiny belt! Goblin: I have no pants. (Entire lower half is missing) Liz: I have a set of magic eyes! Goblin: I already have binoculars.
Liz informing Hellboy that she's pregnant with twins. The look in his eyes just sells it.
Kraus takes over one of the golden soldiers and beats up several others, only to see them reform.
Kraus: Well, I'm out of ideas.
When Abe and Nuala first meet, she insists "Abe Sapien" is not a proper name (he agrees it is a Fail O Sucky Name). She demands he give over his hand so she can use his telepathy to find out. After she does, the embarrassed look she gets is rather amusing.