Chapter 10 of the book "Foundations of Computer Science" (http://i.stanford.edu/~ullman/focs.html) which is available online provides an excellent introduction to automata theory. After that you can start referring to " Introduction to Automata Theory, Languages, and Computation" by Ullman, Hopcraft and Motwani. This is also the reference book for the Automata course (and taught by Ullman) currently being available in Coursera.

I wrote a non-academic book on this subject for the HN crowd: http://computationbook.com/

I took a quick look at Tom Stuart's book and it looks great (thanks for sharing that, Tom! something new on my reading list).

Somewhere in between that and Ullman's stuff in terms of formality is Sipser's Introduction to the Theory of Computation. I like its explanations of the DFA material more than the free Ullman book online, though I haven't read Ullman's dedicated Automata title. (A little too rich for my blood...)