He was in love with rose. In school reunion He even said:
*Rose:* I thought you and me were— Well, I obviously got it wrong. I've been to the year 5 billion, right, but this... Now, this is really seeing the future. You just leave us behind. Is that what you're gonna do to me?
*The Doctor:* No. Not to you.

DEFF.

Amy but not only coz im an eleven & amy fan, i think he really does care for her and i really really love that about eleven (best doctor ever) :)

Except maybe like Rory or Micky.

Amy coz we can all see it I can't exsplan but we can see it

we might like her or not but there's no denying it

you can tell that he respected them all equally but out of them all his love interest was mostly with rose. Martha was definatley close to him but the obvious situation was that he was not over rose and not ready to move on to someone ells, donna and him were more like best friends as they kept repeating over and over that they were just friends, and amy is with rory so yet again her and the doctor are just really good friends.

omg you're kiddin me? there are two different doctors and two different companions, 10 didn't know amy, but 10 and 11 do so its a bit obv people are picking rose just because she was first

Well maybe some people actually think he actually care about rose the most. Not just because she was first.

I don't think he really liked one over the others, they were all good in thier qwn way.

1. Amy
2. He Cares about all them (Donna, Martha, Rory, Donna's Grandfather, Jack, River Song, Mickey, and Rose)

Everybody can see that the Doctor really loved Rose!

1. Rose
2. Amy & Donna & River
3. Clara & Jack & Wilf & Rory
4. Martha & Mickey

Also Amy.