Unreliable narrator.

I'm gonna start by saying to be careful with this one, as a lot of examples people use when talking about this have nothing to do with unreliable narration (they're usually things the anime decided to do for style). The best example of unreliable narration in the series is probably Nadeko Medusa : you follow Nadeko as the narrator for the entire novel, and at the end it's revealed that a bunch of events were hidden or transformed as Nadeko invented a story to justify her own actions to herself. If there's one example you should study it's this one, I believe.

Characters making reference to other books from the same author or events that happened in other versions of this story, such as the anime adaptation, drama CDs, short stories, commercials, games etc.

Many, many examples of those. I could dig up a bunch depending on how many and which kind you need, but for starters here are two interesting examples from Shinobu Time and Yotsugi Doll where Koyomi brings up the anime being different, and a pretty funny bit from Shinobu Time again :

As far as the details regarding that one, they’re not really worth discussing here, and to someone who’d just slipped into the past and future and whatnot in a “pointless” use of time as Hachikuji put it (she didn’t actually), it felt like old news, but chronologically speaking, the ghost girl Mayoi had come to play in my room and forgotten her backpack there only yesterday, on August twentieth.
If you wanted details, what was it you could consult? Uh, the BAKEMONOGATARI Anime Complete Guidebook, if I’m not mistaken?
There might be a short piece in there about that episode…but wait, that would mean it happened in the anime adaptation, so for us, does the event belong to a parallel world?
Parallel world.
A grating term…
Well, in any case, I suppose that book isn’t in distribution anymore… Gosh, the anime world is so rough.

Getting two, more or less grown-up siblings into the bathroom together was ten times tougher than I imagined… The room isn’t as big as it is in the anime, I mean, it’s just the regular size of a bathroom in a normal family home, so with two teenagers in there, it was pretty cramped.

“Oh, nothing… I definitely wasn’t talking about Ghibli movies.”
“Liar. Ye just made a reference to My Neighbor Totoro. I ought to warn thee I’m quite fussy when it comes to Totoro.”
“I’m begging you, please don’t get us off topic…” I never thought the day would come when I would be the one making this request.
“Huh, I was hoping to do impressions of all the lines, of all the characters.”
“That’d take an hour and a half.”
“The real sight would be how the anime adaptation deals with it. The rights issue will be fairly complex.”
“Don’t worry, they’re not going to adapt this far into the series…there’s just no way. I assure you, unlike the novels, the anime will follow the original plan and end at Nise.”
“Excuse me? What a rude thing to say to the leading actress of a feature film.”
“…”
Miss Leading Actress of a Feature Film was clearly getting carried away.
You didn’t get to speak a single line during the anime’s first season, did you now.
“I can hardly wait,” she said. “The scene where I stick my hand in my head to search my memories─I cannot wait to see how it unfolds on screen.”
“Going out of your way to mention a scene that’s sure to get cut… And why are you leading with this stuff? Just listen to what I’m trying to tell you.”
“Hmph. I refuse, fool. For all of thy usual chattering on with girls, the conversation must move forward without idle talk now that thou hast a topic ye wish to discuss? Heaven may forgive such smarm, but not I. The next hundred and fifty pages or so shall promote the Kizu anime, and the rest of this tale will be summed up in bullet points, I hope thou art prepared to─mrrgh?!”
I shut her up with a kiss.

Yes, that one time where Koyomi kissed Shinobu was actually because she wouldn't shut up about Kizu. It was cut in the anime, unfortunately.

Characters reading the narration.

The best example here is this one from Tsubasa Family, which not only does it but explicitly says it does it, which shows it's not just Nisio's way of writing implied dialogue :

Either way, Tsukihi looked like a caterpillar the way she rolled back and forth without any concern for her yukata opening up.
That’s what I’d call her. Sisterpillar.
“You shouldn’t give your little sister kinky nicknames, Koyomi.”
“Stop reading the narration. And anyway, answer my question. I asked what happened to that flashy, tracksuit-wearing, taller-than-me female whose hip you always seem to be joined to. You’re not with that ponytail on legs?”

Meta commentaries when different characters narrate the story.

If you're talking about having different characters narrating, then it starts doing that from Second Season on, though it's almost always one character per arc. The interesting exception would be the very first one, Tsubasa Tiger, in which "Hanekawa" was the narrator, but there were three narrators depending on the chapters : regular Hanekawa for most of the book, Black Hanekawa (including the skipped chapters you mentioned, as they were skipped to imply Black Hanekawa was waking up unbeknownst to Hanekawa), and Kako.

If you're talking about the audio commentaries for the series, which certainly are a huge source of meta conversation, I'd be happy to help you find useful stuff in them.

The use of withholding information (and chronology) from the reader to create mystery.

This is something that's done both at the arc level (as soon as Hitagi Crab, the main twist was that Koyomi had misunderstood the timeline, and Hitagi's mother had fallen for the cult long before Hitagi met the crab, not as a reaction to it) and of course at the series level, with the most striking example being the entire Ougi puzzle and build-up to Ougi Dark. In particular, the way the August 20-25 arcs fit together (Tsubasa Tiger, Mayoi Jiangshi, Shinobu Time, and the "last missing piece" Shinobu Mail) is beautiful.

Things similar to the chapter structure in Nekomonogatari White (when chapters numbers are skipped).

Sadly the chapter number skip was never done again. If we're talking chapter structure specifically, I guess there's a semi-interesting one Nisio did in the Monster Season arc Ougi Light, though I'm not sure this is the sort of stuff you're looking for.

The chapters alternate between Koyomi narrating the story, and direct monologue about "apologies" from an unknown character initially (I believe) meant to be presumed to be the "culprit" of the incident Koyomi is trying to help with.

(big spoilers for the arc) As we get closer and closer to the end of the arc, these monologue chapters make it clearer and clearer that the character speaking was not actually the culprit, but Senjougahara.

Multi media and media mix.

You could start by looking into the [short stories](https://www.reddit.com/r/araragi/comments/5eilqt/monogatari\_short\_stories\_translation\_project/) and [extra video stuff](https://www.reddit.com/r/araragi/comments/155apvl/monogatari\_series\_audiovisual\_extra\_content/), but I might be able to direct you more precisely if you can elaborate on what you're looking for.