Hmm - tricky one this. I see the recent series (Eccleston and Tennant) as so very different from what went before it's comparing apples and elephants. The old doctors had to make do with such crappy sets (I believe at one time the budget for scenery was two hundred GBP/episode), they had to play it tongue in cheek. The new doctors take themselves much more seriously.
If I have to choose one, it has to be Baker (Tom, not Colin), with Troughton getting an honourable mention. Of the recent two, I'd give Tennant the edge - Eccleston is a touch too grumpy. But both are good, and the difference in writers is more significant - give me Steven Moffat over Russell T. Davies any day.