A few. Last is Kimi Raikkonen in 2007, he got the better of the fratricide battle at McLaren, clearly the better car that year.
Another is Rosberg (Keke), in 1982. Ferrari had a dominant car but Villeneuve died mid season and Pironi had a career ending crash later.
I supppse that if you go back a little further in time you'll find more. Reliability played an even bigger part in the outcome of championships, so the best car might not be the fastest, but the strongest back then.