So many great quotes.
Everything from Saren and Shepard's conversations. Those were the best dialogues I've seen in any game. The whole thing felt very real, two people trying to convince each other (and themselves, in Saren's case) that the path they've chosen is the right one. It would probably be easier to just post a youtube video, but I'll choose a couple lines.
Saren: My mind is still my own... for now. But the transformation from ally to servant can be subtle. I will not let it happen to me.
Shepard: Sovereign's manipulating you and you don't even know it! You're already under its power!
Saren: No! Sovereign needs me. If I find the Conduit, I've been promised a reprieve from the inevitable. This is my only hope.
Shepard: Together we can stop Sovereign. We don't have to submit to the Reapers. We can beat them!
Also, Sovereign's entire speech on Virmire, but especially these lines -
"You exist because we allow it. And you will end because we demand it."
"Our numbers will darken the skies of every world."
"Your words are as empty as your future. I am the vanguard of your destruction. This exchange is over."
Here's more quotes, in no particular order.
"In the darkest hour, there is always a way out."
"It only takes one candle to light a fire. And then the darkness is no more."
- Eve/Bakara
"I want you to know that no matter what happens... You've been a champion to the krogan people, a friend to Clan Urdnot... and a brother/sister to me. To every krogan born after this day, the name "Shepard" will mean "hero!" Now let's show them why!" - Wrex
"You’re unique. Not just in ability or what you’ve experienced, but in what you represent. You stood for humanity at a key moment. You’re more than a soldier - you’re a symbol. And I don’t know if the Reapers understand fear, but you killed one. They have to respect that." - TIM
"Shepard, you died fighting for what you believed. I brought you back so you could keep fighting." - TIM
And an honorable mention to one I just found out about recently here on the forums, if Jack is not present for Grissom Academy.
Shepard: They lost a fellow soldier, and they'll fight to honor his name.
Rodriguez: What the hell good is that? He won't be there.
Shepard: His memory will be. Use it. Get angry. Someday that anger will be the only ammunition you have left - and Jason Prangley's going to save your life again.
Well, that turned out to be a wall of text. And I had to narrow it down a lot. There are so many other great quotes in this thread too. Okay, just one more that made me laugh because it's so fitting for my first Shepard.
Parasini: You can't bludgeon your way through bureaucracy.
Shepard: I can bludgeon pretty hard.