This is a list of my personal favorite story per season/series/block of episodes. Feel free to comments your favorite or any disagreements you have.
Season 1: The Keys of Marinus (I know it's not the most iconic story of season 1 but it's just really scifi goodness)
Season 2: The Dalek Invasion of Earth
Season 3: The War Machines
Season 4:The Tenth Planet
Season 5: The Tomb of the Cybermen
Season 6: The Mind Robber
Season 7: Spearhead From Space
Season 8: Terror of the Autons
Season 9: The Sea Devils
Season 10: The Three Doctors
Season 11: The Time Warrior
Season 12: The Ark in Space (much better than Genesis)
Season 13: Pyramids of Mars
Season 14: The Deadly Assassin
Season 15: Horror of Fang Rock (I honestly wasn't too impressed with season 15 as a whole.)
Season 16: The Pirate Planet (Possibly my favorite Tom Baker story)
Season 17: City of Death (I count Shada as part of this season but still prefer City of Death)
Season 18: Logopolis
Season 19: Earthshock
Season 20: Enlightenment (probably my favorite Davison TV story)
Season 21: The Caves of Androzani
Season 22: The Two Doctors (Not as high in quality as Revelation of the Daleks, Attack of the Cybermen or Vengeance on Varos but I enjoy it more.)
Season 23: The Ultimate Foe
Season 24: Dragonfire
Season 25: Remembrance of the Daleks
Season 26: The Curse of Fenric
1996: TV Movie
Series 1: Bad Wolf/The Parting of the Ways (Weirdly is rarely people's favorite story form this series. That's likely because it's really dependant on what came before so the people who like the dalek storyline of series 1 or more likely to prefer dalek and some people don't like Bad Wold despite it being a really fun and creative episode that's dated in exactly the right way.)
Series 2: School Reunion (It has the return of Sarah Jane Smith and K9 and Anthony Head is great in it. Toby Whithouse is one of my all time favorite television writers)
Series 3:Human Nature/Family of Blood (much better than Blink)
Series 4: Silence in the Library/Forest of the Dead (my favorite Tennant story and one of the most rewatchable)
Tennant Specials: The Waters of Mars (Some of the darkest and most cinematic Doctor Who that exists with really nothing that I can think of wrong with it.)
Series 5: The Time of Angels/Flesh and Stone (A major improvement on Blink with a great atmospheric setting, the return of River Song, a strong guest cast and plenty of seeds planted for later on. My one criticism might be I'd like a slightly more nuanced depiction of religion in the future.)
Series 6: The Doctor's Wife (I love Neil Gaiman and I actually got into the show because I knew he'd be writing for it. The first Doctor Who Magazine I ever bought was focused around this episode.)
Series 7: The Name of the Doctor
2013 Specials: The Day of the Doctor
Series 8: Deep Breath
Series 9: Heaven Sent (This is only technically a two parter)
Series 10: World Enough and Time/The Doctor Falls
Series 11: It Takes You Away
Series 12: Fugitive of the Judoon (Captain Jack and a new Doctor plus the Judoon makes for a fantastic episode,)