In the course I co-teach on Automata, Computability and Complexity Theory we use the excellent videos by Harry Porter to replace our classical lectures, and use our contact hours instead to practice with the material together with the students.
Porter follows the book "Introduction to the Theory of Computation" by Sipser.
A quick google search reveals two courses on the MIT OCW website:
Automata, Computability, and Complexity taught by Scott Aaronson; has Sipser along with two other texts as recommended reading, and comes with lecture notes and assignments
Theory of Computation taught by Sipser himself (!) with the 2nd edition of his textbook as required reading. It comes ...