When I go back to school after Thanksgiving, I'll be taking a course in CS Theory covering topics such as deterministic and nondeterministic finite state machines, turing machines, pushdown automata and a few other things. However, I haven't found a good application that can produce a visual representation of them as well as testing how they work (pass/fail, etc). The best that I've found so far is jFlap, and I'm finding it rather awkward.
It was JFlap that I used in college. I didn't find it that awkward to use, but it looks like it may have changed since then. Sorry I don't have a better answer for you than that.