Ok, here are mine favourites:
"You ever think of writing a book about your exploits in the line of duty?"
"Ah, I've thought about it. But then I'd have to shoot anyone that actually read it." (Hammond and Jack in COTG)
"If you don't make it, can I have your stereo?" (Jack in The Enemy Within)
"You know, we'd have to stick around but some braindead sycophant left my buddy out here to die. So we're out of here." (Jack in The First Commandment)
"Sky... orange?!"
"The sky... up there."
"Yeah, I know what the sky is." (Jack and the native in The First Commandment)
"Carter..."
"No... You can't keep him." (Nafrayu and Jack in The Nox)
"It is only for you." (Kynthia in Brief Candle)
"Oh, my..." (Sam seeing a very naked Ernest in The Torment of Tantalus)
"Catherine, hug me!" (Jack in The Torment of Tantalus)
"You know that's my car, don't you?"
"You should get that window fixed." (Hammond and Jack in Fire and Water)
"Hathor was the Egyptian goddess of fertility, inebrity and music."
"Sex, drugs and rock'n roll?" (Daniel and Jack in Hathor)
"We are the mother of all pharaos."
"Of course we are." (Hathor and Jack in Hathor)
"Is mental illness contagious?" (Jack in Hathor)
"So, what exactly are we going to see after this eclipse begins? I mean, it is black and it is a hole."
"Well, it might be a black hole." (Daniel and Jack in Singularity)
"It's my sidearm, I swear." (Jack in Solitudes)
"Me. Colonel Jack O'Neill. Cumbaya."
"Cumtraya."
"Whatever." (Jack and Harlan in Tin Man)
"Friends?! I don't even like you! Chances are I'll never like you." (Jack in Tin Man)
"For crying out loud." (Jack and his clone in Tin Man)
"Striking an officer is a quick way to a court martial."
"I'm not gonna hit you, Maybourne. I'm gonna shoot you." (Maybourne and Jack in Bane)
"How do I know you're really Daniel?"
"Because."
"Yeah. Okay." (Jack and Daniel in Spirits)
"We came here in peace, and we intend to go in one... piece." (Jack in Touchstone)
"Nyet?" (Jack in 1969)
"And you, O'Neill, you're considered, well you're a pain in the mikta"
"Neck?"
"No." (Aris Boch and Jack in Deadman Switch)
"Maybourne, you're an idiot everyday of the week, could't you have taken just one day off." (Sam in Foothold)