I liked any episodes that included Brigadier Alistair Lethbridge Stewart. The episodes I remember best from the original Dr Who series are The Day of the Daleks. I think Jon Pertwee was the Doctor then. That being said, my all time favourite Doctor has to be Tom Baker.
The episode when he had to erase her mind actually brought a tear to my eye. The actor playing her Grandad who used to keep looking up at the stars, (his name escapes me) was very good.
Liked Amy Pond with Matt Smith, wasn't over keen on the last one, looking forward to see a Female Doctor in the new series.