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 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...

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.