Take two if they say (or imply or subvert) the question "Doctor Who?"
Take a drink any time something is "impossible" or "can't be", etc.
Take two drinks for every one of these during the episode Midnight.
If watching Midnight after midnight, take four.
Take a drink every time Ten says "What?"
On second thought... better only do an episode at a time on this one.
Everytime there is a reference to the work of a famous author or artist in an episode where they appear on the show, drink.
Take a drink every time Jack flirts with someone
Take a drink every time when someone hits on the Doctor, two if he doesn't notice
for Classic Who, take a shot every time something happens of Four's scarf, be it him tripping on it, someone standing on it, or it gets damaged in some way.
Also for Classic Who, take a shot every time K-9 says either "Affirmative!" "Negative!" "Mistress!" or "Master!"
When watching a Gallifrey-based story (particularly The Five Doctors, though The Invasion of Time also works), drink every time someone says the name "Rassilon."
Take a shot whenever anyone says "I'll explain later."
Take a shot every time the First Doctor says "Hm?"