What is the most compatibility-friendly way to add items (any items, really, though I'm interested in spell tomes at the moment) to a vendor? How about to the list vendors get their inventory from? I'd like for these new spells to show up in loot and vendor lists as naturally as the stock spells, if possible, while still being compatible with any other mods that do the same.

Sorry for bumping a thread, but I figured this was better than creating an entirely new one.

Any thoughts at all? Even if the thought is, "You can't do it, because you can't append to a leveled list"?

Well, maybe you can add those books to their inventory at runtime? Set up a quest triggered when your location changes, then on the papyrus side check the location and add books to the vendors of this area.
Note that I am still a beginner myself when it comes to CK+papyrus, so I do not promise this can work that way.

Add them to leveled lists with http://www.creationkit.com/AddForm_-_LeveledItem.

Ah, thank you! I didn't know that function existed. Does that function need to be run at the start of every play session, once per character, or once per computer? If it needs to be run every session, what's the best way to ensure that it happens?

Once per character. Its additions used to not persist across game closing/opening, but Beth fixed it with 1.6

So the best route would be some hidden quest that runs the script, then completes itself so that the script isn't constantly trying to run again? I know I can set a boolean to disable the meat of the script, but doesn't the script keep checking the boolean?

Just http://www.creationkit.com/Stop_-_Quest the quest after it does its thing.

Can you give and example script?

Say for a custom Scroll...

???.AddForm(MyScroll, 1, 1)

Not sure what the ??? would be. Just a property filled with one of the formid for a level list?

And what is the NUMBER for? The number of scrolls that would be generated from the LL? So it cannot be a RANGE like sometimes the vendor has 3 or sometimes they have 1 ?

You can also use the vendor's chest as an Alias, and add the book to the Alias' inventory.

kYourLVLI.AddForm(kForm, 3, 1) ; Add 1 kForm to kLVLI avalable at level 3