I'm studying for an automata test on a course that's heavily based on jflap. Trouble is we don't have much documentation and the sample automata that I've found on jlap like this and this, are insufficient to prepare for the upcoming test.
Where can I find more? Any other resource with sample turing machines shown as graphs with transitions would also be helpful.
"Problem solving in automata, languages and complexity" is a fantastic textbook for anything related to... anything in its title. Among other things, you can find a bunch of examples of DFAs/NFAs/PDAs/TMs for all sorts of things, and they teach you a lot of techniques for building them.
Edit: that first link of yours keeps talking about "nondeterministic NPDAs" and "deterministic NPDAs". I'm writing this edit just to satisfy my urge to denounce such pleonasms and oxymora :)
Try Michael Sipser's excellent book "Introduction to the Theory of Computation". The automata and Turing machines are all expressed as state diagrams, with sufficient text explanation to help you interpret and implement them.
This was our course text at Uni about 4 years ago, just before the 2nd edition came out; it was a real rock, I heartily recommend it!