Toast the seeds all by themselves in a skillet, as though you're toasting a spice. They'll turn golden brown and some of them may even pop. Once they're cooked, add the tiniest touch of olive oil to the pan, just enough to very slightly moisten the seeds when you toss them around, and then season!
I made three batches this afternoon. I seasoned the first with chili powder, cayenne pepper, and salt, the second with lemon pepper, and the third with this insane veggie/parmesan bread-dipping seasoning that I'm putting on everything lately. In a blind pepita taste test (kindly conducted by volunteers Jonathan and Erin), the chili/cayenne/salt beat the lemon pepper by a hair. That's not to say that the parmesan flavor didn't fare well. It was kind of swallowed up by the flavor of the seeds themselves, making it maybe too subtle for this crunchy snack.
I can't wait to throw these on a salad or use them in place of nuts on a cheese plate! Nom, nom! Any other ideas for pumpkin seed seasonings?