Zim

If you would like to sync your Zim wiki database between computers, but don't want to have the plain text version synced (e.g. because of Dropbox/GoogleDrive/OneDrive/Box privacy concerns), you can always save your Zim database file in an encrypted Vault using the excellent open source and cross-platform app Cryptomator.

Otherwise, you can sync using Spideroak, Tresorit, or pCloud's encrypted folder. All of these are end-to-end encrypted.

An additional benefit of using Cryptomator is that you can close Zim, lock the vault in Cryptomator and other users on the same computer won't be able to open or access your Zim database contents.

This solution should be included on the Zim FAQ page, which says that you can't have encryption. This is an easy and convenient solution.

I've been using this for 3 years.

before that, I had used Evernote, Zotero just for making note and have some organized stuff for very long period time.

Since I have found Zim...

I had to move the whole material that I have noted, but It was definitely worth to do.

I'm using Linux mint~ which is perfect for using Zim.

I think there are still some disadvantage of applying Zim to Window OS in some extension.

But I highly recommend this tool, and altering OS to Linux. :)

Speaking of more or less notable feature differences. So, Wikidpad has got anchors, and can also make insertions (you insert content of one page into other, and it updates dynamically when you make changes to the page you inserted content from).
Zim hasn't got this; anchors are planned, but the works for them haven't even started yet.

On the other hand, Zim doesn't have HTML and preview modes, you work in one unified mode; no distorting of downscaled images; somewhat easier and faster work as you don't have to write code.

My personal verdict: if you don't yet have your wikis\notes, then Zim will be easier and faster start. But if you use WikidPad for a long time already and have lots of experience with it - no sense in switching to Zim, as WikidPad has slighly more capabilities.

I have transferred all my notes onto this app, which took me some time, but it was worth the sweat. This app is amazing, the inline preview (displaying nice widgets instantly as you type markup) is really amazing to efficiently take formatted note without breaking your momentum. Also, the Table of Content plugin allows to quickly navigate inside a document, and this has proven invaluable to navigate inside my very long notes. The application is also very stable and relatively memory lightweight (2 processes ~ 30MB total) given it renders all kinds of widgets and support multi-documents.

I gave this a thorough run-through today to see whether it can replace TreePad Lite, which I've been using for over a decade but is getting a little long in the tooth.

Zim is very flexible, especially when you enable the plugins that it supports (my favorite is the Arithmetic plugin that allows inline calculations, e.g., enter "1+1=" and press F5 to get the calculated result). I also like that Zim handles the formatting automatically so you can just focus on the content (e.g., begin a line with "*" or "1." and it will be formatted as a bulleted or numbered list, respectively).

Being a true wiki editor, linking in Zim is as simple as dragging a page (akin to a node in a tree) from the left pane into the document in the right pane (you can also enter a term in CamelCase and it will automatically link). The linkage works both ways, so if you delete a page that has a backlink, all backlinks pointing to it will also get unlinked.

In the end, I decided that Zim was way too powerful for my needs, which is basically organizing notes in a tree view. The price you pay for all this power is memory consumption: this program is pretty heavy. I installed the portableapps.com version and noticed that even when sitting idle it consumes three processes (two Zim processes and one portableapps.com process) totaling about 30 MB. This is way too much for an app that I intend to have running all the time to keep plain text notes. My search for TreePad's replacement continues...

Extremely practical for organizing small notes such as todo-lists and reminders that can be linked.
Saves as plain text files which can be opened by a simple text editor and synchronized with another piece of software.
It has nice plugins for diagrams and math formulas.

I use it with Syncthing which synchronizes my documents across my devices, and Turbo Editor on my Android phone and tablet.

It's an extendable (Python-written) desktop wiki. If you want to own your wiki entries, store them on your Desktop using Zim.

It's fairly good, not all instructions are too clear at first (ie it tells you conflicting information when creating a new notebook, it says you use the same folder, but doesn't tell you it overwrites all the notes in that folder!) has potential and I'm switching from Tomboy to give this a shot,but wont yet delete tomboy as it does simply work with no troubles. But I'm hoping zim will give me a slightly difference approach to note keeping

I tend to do the tags:taggoeshere trick and chase backlinks from the blank filler pages using Alt+B. Using a namespace means I can close the tags namespace and get it out of my face. It's not ideal - hashtagging and a tag cloud or list sorted by frequency would be nicer, plus a search box... idea for a plugin maybe?

Excellent tool for note taking - the journaling features are also extremely good.

Data being stored as plain text makes life easy - I know that I'll be able to access my data in the future if I needed it. Cross compatibility between Windows and Linux is nice, though I struggle with macOS compatibility - though, as plain text, I can edit and view the files on this OS if really needed.

the portable-version from their website will do as expected, however, they need to rework the portable setup, an overwrite of two system-dlls (blocked by antivir-system-protection) can be skipped and ZIM will run anyway on W10, but this is not the way it should be.
btw.: footage in memory is small, that's good.

Real Wiki, searching, linking etc. Text files in some markdown syntax, may be managed like sources with git, subversion etc. This way exchange within a team is perfectly possible. WYSIWYG editor, KISS, e.g. very helpful: copy some snapshot to clipboard, just insert into zim, thereafter resize it as small thumbnail and link it to itself to view it with an image viewer on demand. zim has many useful plugins and customizable parameters. I like it for years now. It's my main tool with dozen of notebooks, context related.

I can't copy/paste text from Zim to other applications...

Great program, but right now WikidPad is my wiki/notebook software of choice.

Edit: the lastest version 0.68 seems to have fixed the issue. I was previously using 0.66

Great.
But still needs some development. For example in shorcuts to add links, equations etc.
The nested number list also needs improvements. Numbering/ordering does not work correctly every time.