Although it's already been said,
Take a drink when a plot arc thing is mentioned (In the Parting of the Ways that probably means you'd be plastered before the kiss (Who fans know what I mean)).
Additional rules would be:
One drink when Doctor9 says 'Fantastic'
One drink when Doctor10 says 'What' or 'Brilliant' or 'I'm so sorry'
One drink when Doctor11 says 'Geronimo!'
One drink when a 'Doctor? Doctor Who?' pun is made
One drink when a companion wanders off.
One drink when a former companion shows up (You'd be half-cut by the end of 'The stolen Earth' and 'Journey's End')
One drink for the TARDIS materialising.
One drink for the TARDIS turning up in the wrong time.
One drink for every time the Doctor gets out his screwdriver to unlock a door.
Oh, and one drink for when a deadlock seal gets in the Doctor's way.
I think that's all bases covered.
Edit: One drink everytime someone says 'Don't blink'.
One drink everytime a Dalek or someone says 'Exterminate' or a Cyberman says 'Delete'