I currently use TiddlyWiki Classic [1]. The sheer simplicity of its UX was what got me to start using it. It has served me well over the years in that I have had no data loss using it with TiddlyFox [2] and the codebase was easy enough to understand and modify when I wanted to customize it beyond the settings exposed to the user. However, as my personal wiki grew and I used it more I found the nonstandard markup and especially the lack of revision history for the individual notes (wiki pages) to be major flaws. The newer version 5.0 release fixes the first one (by introducing Markdown support) but, AFAICT, not the second, which makes the me reluctant to upgrade and lose my modifications to the wiki code. (The downside to TiddlyWiki's approach is that an advanced user ends up effectively maintaining a fork.)

I've looked for alternatives among desktop wikis that run on Linux and my favorite so far is Zim [3]. It uses Markdown and implements history through storing pages as text files in a Git repository. Unlike TiddlyWiki, it doesn't run in the browser. I am considering either switching to it or biting the bullet and setting up a local instance of MediaWiki (or another full-fledged wiki — suggestions welcome!). The latter will likely require more ongoing maintenance but it also keeps the advantages of a browser-based wiki that TiddlyWiki has like embedding images from remote hosts and customizing your user experience with JavaScript.

[1] http://classic.tiddlywiki.com/

[2] https://addons.mozilla.org/en-US/firefox/addon/tiddlyfox/

[3] http://zim-wiki.org/

I use TiddlyWiki for nearly everything (projects, clientele notes, personal notes, code snippets, links) and I'm really happy with it.

I use it on a personal server with SSL (let's encrypt) + auth and works wonders for me. I have an rsync cronjob running every 5 minutes to keep a mirror directory as a backup. The system backup (tarsnap) backups everything anyway twice a day so, I never had any issues.

For anyone else looking into Tiddlywiki, and wanting to get to the meat of it w/o having to read about wiki software etc:

https://github.com/Jermolene/TiddlyWiki5

This is the Tiddlywiki built on Node, and it looks quite good.

Edit: It is currently built on Node 0.8.2, but preparing for 5.1.10, so that's good.