"Bad Wolf" / "Parting of Ways": I don't just dislike, I
DESPISE these episodes!!!
I hate the fact that all the "contemporary culture" references (Trinny & Susanna, Weakest Link, Davina on "Channel 44,000" etc.) went out-of-date so soon after it was made. So parochial and short-sighted of the writers!
I actually threw away my DVD's of these episodes! That's how much I hated it!

Its a shame, because I do like the regeneration sequence at the very end.
"Caves of Androzani": 100% AGREE with what others have said.
Might've worked better as
Tom Baker's finale as originally intended.
"Let's Kill Hitler": Silly plot and unbearable guest character.
"A Good Man Goes To War": Messy, incoherent storyline.
"Turn Left": Find Donna annoying at best of times, so a Donna-focused episode is beyond endurance for me.
"Father's Day": Several reasons... First, 'Nine' was WEAK doctor. Actors like Baker, Smith, Capaldi or Tenant could dignify weak stories; Eccleston sometimes dragged down potentially interesting stories. Second, the CGI flying creatures are inexcusably bad. 2005 wan't THAT long ago! Third, it wasn't moving to me. I don't care about Rose's irresponsible father.
"End of Time": Does this count as a 'popular episode'?
"Time of the Doctor": Matt Smith was fantastic and deserved a better finale than this convoluted mess.
Every-Big-Overblown-End-of -Season-Episode: Especially the Tennant era Master episodes.