The first set of benchmarks comes from the mist2 distribution. The original set of files can be retrieved from Pierre Ganty's mist2 website. The full set of examples can be found here, here, while our selection (essentially, the contents of the PN and boundedPN directories) is available from our site.
Another set of benchmarks was taken out of the examples for the bfc tool from the CProver site. The full set of examples is contained in two files: C program benchmarks and Petri net benchmarks. We selected those examples that were unextended Petri nets; the collection of example is available here from our site.
Lastly, some benchmarks were provided internally. They are available here.
We also provide a set of all benchmarks used here: complete set of benchmarks.