Rose and Donna. I adore them both for different reasons.
Rose and the Doctor - well she was the first companion I knew, only having seen "New Who" so I think she was everything I thought a companion should be. I liked her fight, her love for the Doctor, and totally fell for her in "Dalek".
Donna and the Doctor - well it was even more special in a way, being linked from the start, the Doctor-Donna. I loved her fire, her feistiness and the fact she was the Doctor's best mate. Nothing romantic at all between them, and her genuine want for him to be happy, especially when he saw Rose again. None of the childish jealousy like with Rose and Martha.
Martha I really didn't like. I don't think Freema was right for the role of companion, I found her wooden and not very believable. There was no chemistry between her and DT, and the lovesick puppy thing was irritating, whereas I found it very believable with Rose, especially with CE.
So, Donna probably edges it for me in terms of being the best companion for the Doctor. She was older, more mature and funny, but my favourite is Rose.