The clear leader for me is Season 5, as I fucking
adore Matt Smith's Doctor and the stories were almost universally great. I don't even have a problem with "Victory of the Daleks," as it was a necessary hour-long handwaving in order to un-fuck the Daleks so Moffat can use them without having to come up with increasingly convoluted bullshit in order to explain their appearances.
Trailing
just behind would be Season 1, as "Boom Town" is the only really execrable episode of the year. Everything else is, at the very least, pretty good (even the fucking Slitheen two-parter). "Dalek," "Bad Wolf" / "The Parting of the Ways," "Father's Day" and "The Empty Child" / "The Doctor Dances" are all fantastic.
Season 4 was the next-best year, as it had a great companion and some really great stories. While "The Stolen Earth" / "Journey's End" were a clusterfuck of Biblical proportions and I'll stab someone if I ever watch "The Unicorn and the Wasp" again, as a run it was largely entertaining. My biggest complaint, outside of the three episodes already mentioned, is the utterly shameless transformation of the Doctor from a somewhat-lonely traveler into KING SHIT OF TIME MOUNTAIN. Parts of stories got entirely too self-indulgent with "oh, shit, the Doctor is awesome, let us all suck his dick," and it sometimes detracted from the overall storytelling quality.
I'd then say that Season 3 comes up in the next place. This was the year when "SAVIOR OF THE UNIVERSE" Doctor really started to come out as Davies just decided to express his fetish for Tennant on the page, but there were still some really,
really good stories, such as "Human Nature" / "The Family of Blood," "Blink," "Gridlock" and "Utopia." It's a decent year, but there are too many clunkers, especially "42" and "The Shakespeare Code" (Gareth Roberts

). The other complaint is that Martha Jones is essentially Rose Tyler with a medical degree. The entirety of her character's throughline is "I'm in love with this 900-year-old guy but I'll never say it. Oh, and I'm a doctor."
Season 2 is, by far, the worst. I'm really surprised I liked Tennant so much after such a woeful year. The only stand-outs are "The Girl in the Fireplace," "Doomsday" and "The Impossible Planet" / "The Satan Pit" (the last of which may well be my favorite New Who story). Davies turning the show into a
Buffy-esque melodrama with Tennant and Piper fawning all over one another as though they were freshmen in college, plus utterly unforgivable crap like "Love & Monsters" and "Fear Her" ... I just don't find it a really re-watchable season.