I'm going to do something different, and say what my favourite individual episodes are.
1. Terror Of The Zygons: ep 1 - Classic Who always did atmospheric, mysterious first episodes like no other show, and this is the best of the bunch for me. Tense and foreboding, the characters you meet are off-kilter somehow once you get over the cliched Scottish nonsense. And what a reveal, and cliffhanger!
2. Robots Of Death: ep 2 - "Do that again and I'll cripple you", "A simple no would have been sufficient", "You're a classic example of the inverse ratio between the size of the mouth and the size of the brain" - an eminently quotable episode. It also ratchets up the paranoia, and the bit when Poul says he'd call for a robot and realises the Doctor might be right is chilling, even though we knew it all along.
3. City Of Death: ep 2 - also stupidly quotable, it's the timey-wimey stuff I love here. The cliffhanger is a genuine game-changer, and a definite WTF! moment. Suddenly all bets are off.
4. Genesis Of The Daleks: ep 5 - while generally I find this story a little padded, it does contain two of the finest moments of Dr. Who, the twinned genocide questions. While the more famous one comes in episode 6 ("Have I that right?"), I love the Doctor-Davros version in this episode, where Davros shows his true ranting colours. Shocking cliffhanger though.
5. Logopolis: ep 4 - this was a tough choice, but I've chosen this just for my 9 year old self and the passing of my favourite Classic Doctor. I thought the Watcher was a really good idea, suitably enigmatic (i.e. not explained in the slightest), and the old friends and foes regeneration was inspired.