<p>This is a tricky one and I've always relied on techniques, such as permission-based emails (i.e. only sending to people you have permission to send to) and not using blatantly <em>spamish</em> terminology.</p>

<p>Of late, some of the emails I send out programmatically have started being shuffled into people's spam folder automatically and I'm wondering what I can do about it.</p>

<p>This is despite the fact that these particular emails are not ones that humans would mark as spam, specifically, they are emails that contain license keys that people have paid good money for, so I don't think they're going to consider them spam</p>

<p>I figure this is a big topic in which I am essentially an ignorant simpleton.</p>

You can tell your users to add your From address to their contacts when they complete their order, which, if they do so, will help a lot.
Otherwise, I would try to get a log from some of your users. Sometimes they have details about why it was flagged as spam in the headers of the message, which you could use to tweak the text.
Other things you can try:
Put your site name or address in the subject
Keep all links in the message pointing to your domain (and not email.com)
Put an address or other contact information in the email