I've gotten advice from a lot of people (including employers!) to apply to jobs even if I don't have every skill listed in the job description. (I've also heard that men are much more likely to apply to jobs that they don't meet all the requirements of. Side note.)
At the same time, I don't want to waste a company's or my time.
Are there any rules I can follow to determine when it's okay to apply to a job that I'm missing a couple "required" skills and when I should pass?
Unfortunately, it's one of those "it depends" situations. You really have to use your judgement. Here's how I'd think of it: required skills listed in a job are what the hiring manager/company think are necessary to get a certain job done. I think that means that you can potentially still help that company get that job done, but maybe with a different set of skills or only with a few of the skill sets they've listed. For example, a job requirement might list that product manager needs to be amazing at SQL to do well, but a candidate with extensive UX experience might be able to do just as well, if not better.
One rule that could be valuable is to probably steer away from roles that would entail managing other people if you're not personally prepared to manage people. I'd say the average early-career candidate isn't prepared to manage others yet, so they should probably avoid roles of that nature. Similarly, roles that may not require people management, but require ownership of a product/project may not be well-suited for someone that is still looking to learn how to contribute to, let alone manage a project.