The Obligatory Monty Python References

Dantia: "Shepard? But you're dead!"
Shepard: "I got better."
Garrus: "Wait, what? Really, Commander? Are you seriously that droll about this?"

And then there's mine:

EDI: "Data from the Collector ship has been decoded. The Collector base is located in the ...aaaaagghhhhh Nebula."

Shepard: "I'm a Spectre. Start talking."
Elias Kelham: "Well I didn't vote for you."
Shepard: "You don't vote for Spectres! The Council decreed it!"
Elias Kelham: "If I went around calling myself above the law, because some holographic aliens told me I was a ghost, they'd put me away!"
FLASHY RED STAR
RIGHT TRIGGER
*smack*
Elias Kelham: "Now we see the violence inherent in the system! Help! Help! I'm being repressed!"

Joker: "Take a look, Commander."
Shepard: "We'll have to give her a name."
*cool music*
Jacob: "Welcome to the new Normandy."
Shepard: "It's only a model."
Joker: "Shhhh!"

Shepard: "On second thought, let's not go to the Citadel. It is a silly place."

The Illusive Man: "There are some who call me... TIM."