Unfortunately, I lack experience with the original Doctors and like so many people only have experience with the reboot, so please understand that my ability to select is based entirely on the new series.
1. Donna Noble
Of any of the new companions, except possibly Rory, she had the roughest time and more reasons to look at her spaceman say "Enough of this bollocks I want to go home" than any of them and yet she perseveres, still yelling at the world to change (and somehow making it listen) until she is no longer physically capable of remaining. Even then, it's obvious that she really would have preferred to die as a companion than to return to a life of mediocrity.
2. Rory Pond
First, I know he hasn't technically taken her name and keeps wishing she'd take his, but let's face it, that will forever be who he is. More importantly, he's had a significant amount of development from curious nurse to the Centurion and as the most recent episode shows is still growing in awesome.
3. River Song
Fun, mischievous, tragic, and able to stand toe-to-toe with the Doctor. Enough Said.
Honorable Mentions:
Captain Jack Harkness: Just self-effacing enough to keep from becoming an arrogant prick
Amy Pond: Completely awesome, but occasionally smells slightly of Mary-Sue. . .
