My ranking:
4
2
1
3
Season 4 had Donna, played by the wonderful Catherine Tate. Honestly, I think she's the only companion actress who was able to keep up with David Tennant. And since Donna was able to carry more of the comedy in Season 4, this allowed Tennant's Doctor to calm the fuck down. (At one point, I loved Tennant's manic energy but after a while it gets to be a bit much.)
Highlights of Season 4: "Partners in Crime," "The Fires of Pompeii," "The Unicorn & the Wasp," "Silence in the Library," "Forest of the Dead," & "Midnight."
Clunkers of Season 4: No real clunkers to speak of. I didn't care for the Doctor's self-righteous speech at the end of "The Doctor's Daughter." And things did get way too overblown with the Daleks' destroy-reality-itself plan and yet another genocide of the Daleks ending. However, I'm a sucker for crossovers, especially giant crossovers, so the appearances of Sarah Jane Smith, Luke Smith, Captain Jack Harkness, Gwen Cooper, & Ianto Jones all ultimately leave "The Stolen Earth"/"Journey's End" in the plus column for me.
Season 2 I'm a fan of because I was still greatly enjoying Tennant's manic energy at this point. There were some great stories and I thought Rose's departure was handled beautifully. (Unfortunately, Rose's excellent departure has since been marred by her numerous angsty name drops in Season 3 and by the new tacked on happy ending in Season 4.)
Highlights of Season 2: "The Girl in the Fireplace," "Rise of the Cybermen," "The Age of Steel," "The Impossible Planet," "The Satan Pit," "Army of Ghosts," "Doomsday," the last 20 minutes or so of "The Christmas Invasion."
Clunkers of Season 2: "Love & Monsters" & "Fear Her" are totally unwatchable. "New Earth" isn't very good either.
Season 1 has a flawless record but just doesn't reach the same kind of epic highs as Season 2. Possibly the best 1st season of any sci-fi show ever.
Highlights of Season 1: "Dalek," "Father's Day."
Clunkers of Season 1: None.
Season 3 was the worst. I like Martha but the writers never seemed able to write her well.
Highlights of Season 3: "Human Nature," "The Family of Blood," "Blink," Captain Jack coming back.
Clunkers of Season 3: Everything else. Most of Season 3 could be the victim of a 1970s style BBC purge and it would not be any great loss. I'd gladly toss out everything from "Gridlock" through "42."