What do you call the little plastic dowel-like protrusions that keep two pieces of plastic together?

Boss In engineering, a boss is a protruding feature on a workpiece. A common use for a boss is to locate one object within a pocket or hole of another object.

See the pictures from this search for examples like yours.

Let me elaborate for you with this update:

Here is a fairly comprehensive book on plastic part design that covers bosses and other plastic part features in great detail. It’s a searchable book, and you might find it helpful for what you are doing.

Boss is the generic name given to the protruding feature in a mechanical design. As you recognize, the function of that protuberance varies, and it can be a protruding pin or a reinforced hole (or a protruding pin with its own hole (See here).

Terms like locating pin or tab and locating hole or slot are common. Pilot holes (in a boss) accept screws or threaded inserts. I haven’t seen any authoritative mention of terms like “male boss” and “female boss”. You can search the above-mentioned book yourself for terms that are used.

Bosses aren’t limited to plastic design, and any fabricated item might have a boss. The boss might be inserted into a second part in an assembly, fastened by whatever means the designer chooses (e.g. screwing, welding).

"Pin" is the term used for the jewel case hinged apparatus, per the details in the jewel case's patent:

. . . "The standard CD Case as a whole is asymmetrically formed around the optical disk which it holds, so that the holes and the pins forming the hinge are formed in such a case beyond the area required to contain such optical disk."

In an automotive context, your “flanged cylinders” are referred to as panel clips or trim clips. However, those are somewhat generic terms, and take in several varieties of clips. More-specific terms include panel clips, dart type; door trim panel clips; headlining trim clips. (Images 1, 2)

For the projecting pegs, I have heard or seen them called stanchions (“vertical pole, post, or support”) most commonly, and sometimes posts, pegs, or (as Reddast mentioned) tenons.

I'd probably call them barbed plugs. That search shows at least some others do too, so it would be a reasonable way to start looking if you wanted to buy some.

barb - a subsidiary point facing in the opposite direction to the main point ... intended to make extraction difficult.

You might also get somewhere if you searched for press-in plugs (or fasteners).

Some of the things in OP's pictures don't seem to have any special features designed to prevent the fastening from easily coming undone. Any such "passive" fixing is really just a type of locating lug.