The 3rd doctor is probably my least favourite of the Doctors - I think he's pompous, humourless and generally acts like he wishes he could be a Victorian gentleman instead of a time travelling alien.
That said, I love his first series, especially Inferno, and I'm quite fond of The Green Death. Does anyone else have a favourite Pertwee?
The first season just really has a different feel - there's a lot more actual tension between the Doctor and the Brigadier for instance.
As for Mike Yates the first story I ever saw him in was Planet of the Spiders!