As a counterpoint to Hopcroft+Ullman, from another who has not read other books, Problem Solving in Automata, Languages, and Complexity by Ding-Zhu Du and Ker-I Ko was terrific. I did it as an undergraduate independent study class, completely from this book, and found it to be easy to follow if you are willing to work through problems.
Maybe we need someone who knows something more on the subject?
On systems theory, I’ll recommend “Thinking in Systems: A Primer” is a great general audiences book, with a great nontechnical approach.If you are looking for something more mathematical, you’ll need to ask someone else; I’m just not well read enough. (Despite being a math major back in school.)
“The Fifth Discipline: The Art & Practice of The Learning Organization” is a great book, but not as useful for systems theory in general, it’s a more domain specific book. (I would recommend it, but not as the best book on the subject generally)
“Introduction to Systems Thinking” by Kim is just not as good; it’s a fine book, but small and not at all comprehensive.
There are some great, slightly more technical books on the subject, like An Introduction to General Systems Thinking by Weinberg, as well, I am sure, as others. I haven’t read enough of them to say that that specifically stands out among technical books on the subject. (If anyone has recommendations on the technical side, I’d love to hear them, as I would like to see more.)