I'm not clear if you are looking for books, links, or topics. If you are looking for topics or books, I'd suggest starting by taking a look at the syllabi from degree programs that you respect. You may want to pay particular attention to the courses that have the word "Theory" and "Computation" in them.

You are going to find topics like:

  * Regular Languages/Expressions
  * Automata
  * Nonregular Languages
  * Context Free Languages
  * Turing Machines
  * Decidable vs. Undecidable Problems
  * Halting Problem

You can probably get a long ways just doing some searches for those topics.

I written about some of these topics in an article last year that might give you a very small introduction to finite state machines: http://blog.markwshead.com/869/state-machines-computer-scien...