Well, in terms of amusement value there are just so very many! I think one of my favourites must certainly be the exchange between the Doctor and Skagra in my signature, but as far as other quotes that are meaningful or beautiful, I have several:
From 'The Moonbase'
The Doctor: There are some corners of the universe which have bred the most terrible things. Things that act against everything that we believe in. They must be fought.
From 'The Tomb of the Cyberman'
The Doctor: Our lives are different from anybody else's. That's the exciting thing. Nobody in the universe can do what we're doing.
- I also have to say, I think that the whole conversation between the Doctor and Victoria here is quotable as one of the greatest exchanges in the history of the series.
From 'The Wheel in Space'
The Doctor: Well, it's an interesting theory...
Zoe: Oh, it isn't a theory. You can't disprove it. It's pure logic.
The Doctor: Logic, my dear Zoe, merely enables one to be wrong with authority.
From 'Inferno'
The Doctor: Listen to that! It's the sound of the planet screaming out its rage!
From 'Planet of the Daleks'
The Doctor: Courage isn't just a matter of not being frightened, you know. It's being afraid and doing what you have to do anyway, just as you did.
From 'Invasion of the Dinosaurs'
The Doctor: It's not the oil and filth and the poisonous chemicals that are the real cause of pollution, Brigadier. It's simply greed.
From 'The Ark in Space'
The Doctor: You haven't touched anything have you Harry?
Harry: What, me?
The Doctor: Well there are only two of us here and your name is Harry.
From 'Planet of Evil'
The Doctor: You and I are scientists, Professor. We buy our privilege to experiment at the cost of total responsibility.
From 'The Face of Evil'
The Doctor: You know, the very powerful and the very stupid have one thing in common. They don't alter their views to fit the facts. They alter the facts to fit their views. Which can be uncomfortable if you happen to be one of the facts that needs altering.
- This was my forum signature for a very long time.
From 'Horror of Fang Rock'
Lord Parmadale: Are you in charge here?
The Doctor No, but I'm full of ideas!
From 'City of Death'
Duggan: You can't make an omelette without breaking eggs.
Romana: If you made an omelette, I'd expect to find a pile of broken crockery, a cooker in flames, and an unconscious chef!
From 'Earthshock'
The Doctor: Emotions have their uses.
Cyber Leader: They restrict and curtail the intellect and the logic of the mind.
The Doctor: They also enhance life. When did you last have the pleasure of smelling a flower, watching a sunset, eating a well-prepared meal?
Cyber Leader: These things are irrelevant.
The Doctor: For some people small, beautiful events is what life is all about!
From 'Frontios'
The Doctor: What I think, and you did ask what I think…
- Not just this line but the entire tirade where he utterly reams Plantagenet a new one was possibly
the best fifth Doctor moment!
From 'Attack of the Cybermen'
Doctor: The TARDIS, when working properly, is capable of many amazing things. Not unlike myself.
Doctor: I've already told you. I am known as the Doctor. I'm also a Time Lord from the planet Gallifrey in the constellation of Kasterborous.
Russell: You're bonkers.
Doctor: That's debatable.
From 'Trial of a Time Lord - The Mysterious Planet'
Doctor: Planets come and go. Stars perish. Matter disperses, coalesces, forms into other patterns, other worlds. Nothing can be eternal.
From 'Trial of a Time Lord - The Ultimate Foe'
Doctor: In all my travelling throughout the universe I have battled against evil, against power mad conspirators. I should have stayed here. The oldest civilisation: decadent, degenerate, and rotten to the core. Power mad conspirators, Daleks, Sontarans... Cybermen, they're still in the nursery compared to us. Ten million years of absolute power. That's what it takes to be really corrupt.'
From 'Ghost Light'
Ace: Don't you have things you hate?
The Doctor: I can't stand burnt toast. I loathe bus stations. Terrible places. Full of lost luggage and lost souls.
From 'Survival'
The Doctor: There are worlds out there where the sky is burning, where the sea's asleep and the rivers dream, people made of smoke and cities made of song. Somewhere there's danger, somewhere there's injustice, somewhere else the tea is getting cold. Come on Ace. We've got work to do.
These are just some of my favourites. I couldn't think of them all.
Perhaps more to come!
Love!
Hushicho
I did like that quote although the scene was absolutely daft, who runs out like that in a time not their own, without any of their belongings or anywhere to go? As I said before, that scene only works if you think about the Doctor carefully going around to make things possible for her. 
)
