I remember it clearly in 1996 when it came on the TV that he had died, it was kind of a shock. Being 11 years old I don't know if I was fully aware which Doctors were alive and which weren't. It's not exactly the funnest Dr Who trivia to research.
My fave Jon Pertwee stories are Spearhead From Space (for me easily the best debut story of any Doctor), Inferno (it fully deserves it's 7 episode length, in fact with the imagination that came with it, it could have gone on for even longer), The Sea Devils (one of the first Dr Who stories I bought on video), Curse of Peladon (I always did love a good old murder mystery), Claws of Axos (loved the feeling of unease the humans had whether to trust such a powerful and unusual alien) and Frontier in Space (it feels like 3 stories wrapped into one).
But my favourite of all is The Daemons, maybe because I like the Satanic elements in the story, with giant Azal and his goat legs and Bok the stone gargoyle.
I think I actually heard it was Jon Pertwee's favourite aswell. I'm not surprised, what with the cute village setting, the dynamic characters, especially seeing UNIT out of their uniforms for alot of the time, and the constant discussion of science vs magic.
What I love about his Doctor is that he was actually the most active one if you think about it, despite being one of the oldest actors to take on the role. Even the younger Doctors probably didn't get into as many fights as the 3rd Doctor did.

He took Dr Who into the land of colour TV and the cool, stylish 70's.