Sorry to take a while to reply, I had to think! Note that old who serials and New Who two-parters count as one in this, so basically I'm looking at Doctor Who stories rather than episodes. I doubt many people are going around professing their love for Episode Three of An Old Serial. :-D
So, current list, which may be different in a different month or something.
1. The Enemy of the World (1967, Second Doctor era) 2. The War Games without the last 10 or so minutes (1969, Second Doctor era) 3. The Empty Child/The Doctor Dances (2005, Ninth Doctor era) 4. Mind Robber (1968, Second Doctor era) 5. Utopia (2007, Tenth Doctor era)
Note: There are a lot of Classic Who stories I haven't yet seen. As can perhaps be seen, I've watched the Second Doctor era more extensively than others. (I wanted to include stuff from other Classic Doctors, but well, that would have to be a top ten, I just couldn't not include those three stories.) The Moffat era suffers in comparison to earlier eras because I've only got around to rewatching a few of the stories from it. (And we're not speaking of you-know-whose era.)
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So, current list, which may be different in a different month or something.
1. The Enemy of the World (1967, Second Doctor era)
2. The War Games without the last 10 or so minutes (1969, Second Doctor era)
3. The Empty Child/The Doctor Dances (2005, Ninth Doctor era)
4. Mind Robber (1968, Second Doctor era)
5. Utopia (2007, Tenth Doctor era)
Note: There are a lot of Classic Who stories I haven't yet seen. As can perhaps be seen, I've watched the Second Doctor era more extensively than others. (I wanted to include stuff from other Classic Doctors, but well, that would have to be a top ten, I just couldn't not include those three stories.) The Moffat era suffers in comparison to earlier eras because I've only got around to rewatching a few of the stories from it. (And we're not speaking of you-know-whose era.)