Personally for me its between Spearhead from Space
and The Eleventh Hour
. Both are post regeneration stories that are reinventions of the show. The exile on Earth is my favourite era and its a great story to start off Pertwee's Doctor. Equally The Eleventh Hour
was the first attempt to reinvigorate Doctor Who since its return with a multitude of changes to the cast and a new senior production team with a different take on the program (i.e. the lonely god vs. the madman with a box).
Its fair to say they both stories hit the nail on the head but I have to give it to Spearhead