3 of his movies which have remained with me and which I think were his best in terms of acting skills were Swades, My Name is Khan and Chak De India. They might not be his biggest block busters, but he did make sure he touched a chord within me in each of them.
Swades the first one of them was a commercial failure, not everyone's cup of tea and definitely not mainstream.The story of Mohan, trying to find his nanny from yesteryears after spending most of his youth and adult life in the US was something thought provoking. What touched me is his act when he interacts with the villagers and the poorest of the poor in India. There is this one scene where he goes to collect rent from someone - and finds how life actually is. There is this particular sequence where he is in a train, while a boy outside is vending drinking water for 25 paise (Rs. 0.25). There is no dialogue, but his face and eye expressions were priceless. Gives me goosebumps even today when i think of the economic disparity in India exposed in that one scene.
My Name is Khan is another stunner - as he handles both religious and racial discrimination in his quest to meet POTUS, as he seeks retribution for the death of his son due to a fight as a result of religious discrimination in the aftermath of 9/11. He is also handicapped by a disorder which limits his ability to interact and emote. This one did well overseas , and decently in India too. The whole movie is a treat - and shows how a man who shrugs off negativity thrown his way to come up a winner against a system prejudiced against him.
Chak De is the most commercially successful of this list (at least in India). In this one the script itself does a lot of the work and the support cast is great too. However the story inspired by true events ( former Indian field hockey player Negi) of a man who got accused of throwing away a match due to his religious background. Years later, still bearing the scar of that accusation he comes back to coach the women's team to word cup glory. Scene of the movie for me? Probably the end when he visits his old home.