Actually, leaving aside missing stories, I think that there are only maybe four stories that I haven't watched. I know I haven't watched The Reign of Terror (okay, so that has two episodes of six missing, but it's being released on DVD with animated episodes soon), Planet of Giants, and The Doctor, The Widow, and The Wardrobe, and maybe Nightmare of Eden.
Of episodes available from missing stories that I haven't watched, I haven't watched Galaxy 4: Airlock and The Underwater Menace episode 2 (for obvious reasons, as they were only discovered recently), The Faceless Ones episodes 1 and 3, and The Web of Fear episode 1.
All you need to understand
Is everything you know is wrong!
-Weird Al Yankovic