I just cooked up some squash seeds and they were delicious. Here is my recommendation. This is loosely based on Mark Bittman's advice in How to Cook Everything Vegetarian
I started with a smallish buttercup squash. I think this recipe would apply equally well to butternut squash or pumpkin seeds. I sliced the squash in half along its hemisphere(?) (its prime meridian? whatever man) and scooped out the seeds and the surrounding goop. (Basically, inside a squash there are two kinds of flesh, the firm flesh that adheres to the skin, and the goopy flesh that occupies the hollow chamber and contains the seeds. I scooped out the goopy stuff, scraping it from the firm flesh.)
I then separated the seeds from the goop. This is the messy, laborious part of the job. I wish I had measured the amount of seeds I got, but it was maybe... I don't know, half a cup? Maybe a little less? This is painstaking work, I basically had to remove the seeds one by one (the goopy, stringy flesh tends to cling to them). A little bit of squash stuck to the seeds is tolerable, though, so don't drive yourself crazy with this step.
I put the seeds in a bowl and covered them with warm water. The point was just to dissolve some of the goop that still clung to them. After maybe 10-15 minutes, I poured the seeds through a colander and then put them back in the bowl (which now had no water in it). Then I added 1/2 cup of water and 1 tablespoon salt, stirring it around a bit to dissolve the salt and form a very salty brine. (The seeds ended up very salty, which I found delicious. You could reduce the salt quite a bit if you don't care for really salty results. I will probably use more like 1.5 or 2 teaspoons next time, which I still expect to be quite salty. But note that the ratio of salt to water is probably the relevant factor. If you have to use more water to cover the seeds, adjust the salt accordingly.)
I let the seeds soak in the brine for maybe half an hour. Then I poured them through a colander again but did not rinse them. I heated a tablespoon of olive oil in a frying pan over medium-low heat. Then I added the (still wet with brine) seeds and stirred them—they hissed in the hot oil. After a few minutes of stirring, I spread them out over the bottom of the frying pan and left them over low heat. I stirred them a few more times, every few minutes, and after a total of about 12-15 minutes of cooking they were starting to brown up. I removed them from the heat, let them cool down a few minutes, and ate with no further seasoning.
They were delicious. They had a nice popcorn-like character. I devoured all of them in like two minutes. Oh man, they were so good. It's my new favorite snack. (One thing is, they were pretty oily. I ate them with a spoon, so my hands wouldn't get all oily. You could probably use a bit less oil, but I bet they would still be somewhat messy to eat by hand.)
One variation would be to skip the brine and salt the seeds directly in the frying pan. That would probably use less salt, which I guess would be economical (though salt is pretty damn cheap). I'll try that sometime and see how it works. My concern would be that the saltiness would be less evenly distributed. But I mean, it would probably still be delicious, maybe even more so.
One problem is that the ratio of seeds to squash is such that you'll have to eat a fair amount of squash if you want to enjoy the seeds very often. But I mean... squash is great too. I will experiment with how well the seeds keep once they've been removed from the flesh, and once they've been fried. But I doubt I will very often be able to resist eating them all at once.
You could easily season them however you want. Pepper, garlic, whatever. They were fantastic on their own, though, with nothing but the salt and the olive oil to flavor them. You could also probably put them on top of various savory foods as a garnish type thing. But again... they were amazing on their own.