How to communicate well.

How to think for yourself (and especially, what problems are worth solving that others are ignoring).

How to build stuff (and especially, how to get things done instead of just talking about getting things done).

How to learn new things quickly.

What do you think are the right tools to get these skills ? Books ? (Which ones ?) University/Online courses ? (Any recommendation ?) Else ?

You might find http://parrotread.com/yc useful. It has book recommendations from all YC partners, including Sam.