You should not crack your knuckles during prayer; for Ali, may Allah be pleased with him, said that the Prophet, peace be upon him, said: "Do not crack your knuckles while you are in prayer." This is found in Sunan Ibn Majah 1: 310, Musnad Al-Bazzar 3: 84, and others. The narrators of its chain are trustworthy. See: I'laa as-Sunan 5: 110. See: Al-Bahr ar-Ra'iq 2: 21, Kanz ad-Daqa'iq 1: 163, and Durar al-Hukam 1: 107.