Rashi: It means that Hashem drew everyone to him - he found favor in everybody's eyes.

Ohr ha'Chayim: Hashem put his Shechinah on him, and automatically he had grace in the eyes of all.

Malbim: Hashem caused Yosef to be established to be innocent, and afterwards gave him grace in the eyes of all, even though the chief prison warden [normally] acts based on habit (he engages in cruelty).

Ha'amek Davar: Va'Yet is above nature. Normally, there is no grace and Chesed among prisoners - they are criminals and thieves! Even so, through Hashgachah, there was grace on Yosef; all the inmates did Chesed with and honored him.