My absolute favorite is The Doctor's theme from seasons 1 and 2. It changes a little in the next few seasons with Ten. I love how mysterious is sounds. I think it fits with the mystery of time.
My next favorites would have to be the opening and ending credits themes.
This one is from season 5, I prefer the ones from the earlier seasons though.
This is the one that I really like!
I really enjoy I Am The Doctor as well. There is this building excitement of it in the beginning that is repeated but just makes me simile. There is just something about it.
Those are my favorite Doctor Who sound tracks. I am not particularly familiar with all of the tracks though I have notices that I have never been displeased with any of the music that I have heard.