In chapter 3 Dr. Farmer's use of the word comma was his way of expressing anger towards people who were ok with the way money and medicine was distributed in the world.

In chapter 4 the expression "mountains beyond mountains" just means that after ever obstacle there is another one you must face. Also how Dr. Farmer resolved the conflict between medicine and the cultural beliefs of the Zanmi Lasante was he invested time in his patients, he sent them money for food and education. He also got to know them as people not just as patients.