Out of the seasons I have seen (and I certainly have not seen them all as yet), Season 4 of New Who quite definitely gets my vote here! This is the first season of Doctor Who that I watched along with fandom and that certainly helps give it a bit of a boost in the rankings but I'd love this season either way.
Donna is made of awesome and is quite willing to assert her opinion both to the Doctor and to other authority figures she meets. For his part, the Doctor spends much of season revived from his suicidal tendencies of season 3. Oh, he still has issues. I wouldn't love him so much if he was happy and well-adjusted all the time. *g* However, he's much more willing to be a friend to someone else instead of closing himself off and trying to distract the other person with the shiny. And Donna helps him by being both pushy when she feels it's important and ready to give a hug when he needs it.
I'm also a big fan of the theme of the season. No, not the planets disappearing. That's just the surface arc. The true theme of the season is children. Children of the mind; children of the body. I don't think that there was an episode of the season that did not give us a variation of parents and children. From the Adipose in the first episode, to the Sontarans trying to clone themselves all over the Earth, to the Vespiform born out of wedlock: children, reproduction, parenthood. And the finale was all about children -- both of Davros and of the Doctor. It is really too bad that the Doctor's self-loathing got in the way of him being able to appreciate that it is not weapons he turns people into but heroes.