Sasuke's Rinnegan has six tomoe. They indicate that his Rinnegan is "fully charged". If he uses it too often, the tomoe disappear and the Rinnegan needs to recharge. While using the Rinnegan, Sasuke can use his Mangekyo Sharingan as well, but he cannot use either while the Rinnegan charges. So essentially the tomoe don't really mean anything, they're just an indication that the Kekkai Genkai is fully charged.