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I don't have a Zibaldone, but I do like my own wiki (vimwiki) which I love. It's a complete hodgepodge, a place to put links, snippets, stuff to do, whatever. And it's just markdown files under my own control. When I read books on the kindle, I extract any highlights and feed those in too, same for video's I've watched. I wrote a very simple android app (horrible horrible hack) with which to write notes / share links which feeds into the vimwiki. It's great having all the content go into one place, or it is for me anyway.

So yes, I reckon a personal wiki is a modern-day Zibaldone, and I recommend trying one out.

I have a friend who does a simple version of this on GitHub: https://github.com/yoshuawuyts/knowledge

I've been considering doing the same.

Why git? I can't think why I'd want to "roll back". Does he (assuming he by the name) feel the commit history and portability is worth the overhead?
See, I can see why you'd put it in git (because it's easy) but not sure why you'd upload it to the cloud (ie github).
Git allows you to roll back in case you removed something you shouldn't have. The cloud allows it to be easily accessible on your phone, and easily able to be shared should one want to do that.
I like this idea, and I going to do the same.
I've held several jobs which required me to keep an Engineer's Notebook. It was the place were I jotted down all my ideas, thoughts and random pieces of info I needed or found useful. It served 2 purposes:

1. I could go back in time and jump directly to the solution of something that I knew I had solved but couldn't remember how.

2. It was used by my employers to save in case a patent case arose and they had to find evidence pointing to engineers working on a particular idea. For that reason, the notebook had to have sequential numbered pages, entries had to be dated and binding had to be sewn (to decrease the likelyhood of tampering).

Regarding the first point, that can be done using any common note-taking software. I use a mix of Evernote and Zotero. I think both are good but each has its use.

I tried to use a simple Markdown-based folder structure, but it just was too unwieldy for my tastes.

AFter reading other comments here, I realized I've sort of been doing this at work for work related stuff in emacs with org-mode for years. I kind of like the idea of a paper-and-pen version that I carry with me. I mean, I'd rather type it, but not on a phone keyboard, and so the next best portable thing seems like paper and pen.
I've been messing a bit with Orgzly and it's cool, but a bit fiddly (having to press the plus sign to add an entry rather than just typing seems to defeat the spirit for me). I'll likely migrate back to paper/pen, but I'd like to limit the number of things I carry in pockets, and I know I'll have my phone.

What I'd like is some sort of Google Now integration with org mode so I can take notes verbally or quickly with my phone, then revisit them in org-mode later.

Agreed, Orgzly is close. The manual sync thing is weird too.
I use e-mail for this. I have a label in Gmail called "saved", looks like it's got 514 threads dating back to 2004 (when I got a Gmail account). I e-mail the note/link/picture/screenshot/attachment to myself along with a few keywords so I can easily find it later, add the label, and archive the message. Then I get all the power of Gmail search to find it in the future.
Curiously enough I've been using this thing I discovered here on HN a while back called Nuclino for this sort of stuff.

I've rather enjoyed it, though one downside is that it's only 80% portable for me. as in I can't really be bothered to use it with my phone and using it while hiking is a no-go for obvious reasons.

All well and good, that's why I keep Field Notes around for.

Their site is giving me a bad cert error