From the original run, my favourite has to be 'Genesis of the Daleks.'
SPOILER ALERT! SPOILER ALERT!
It gave a great insight into why the Daleks are as they are, and showed the Doctor at his best - a human being would have blown the Daleks up and thought little more of it. The Doctor had the sense to ask what would happen if he did, and chose the harder option, believing it to be for the best.
From the new series, my favourites are generally the ones written by Steven Moffat, because he seems to understand the mechanics of a good DW story better than most, and also makes seemingly everyday things into terrifying nightmares (a child in a gasmask, noises under the bed, statues, shadows... what next?).
I thought my personal favourite was 'Blink,' but I've just re-watched 'The Empty Child/The Doctor Dances,' and they are utterly brilliant. Also they have some great quotable lines.
Goodbye ~:shopgirl:~ - brave heart.