Recs.
Updated
TiddlyWiki, a non-linear notebook for capturing, organising and sharing complex information.
SpecsUpdate
Pros
Pro Active and helpful community typically answers questions within hours.
The official support forum is at talk.tiddlywiki.org. It's frequented by a large number of knowledgeable TiddlyWiki enthusiasts. You rarely see a question go unanswered more than 2 or 3 days, and in most cases questions are answered within minutes. For harder questions, the developer himself frequently wades in to add information.
Pro Encrypt your entire Wiki with SJCL without additional plugins
You don't have to worry about leaving your TW somewhere it might get exposed. You can activate the built-in encryption ability, using the Stanford Javascript Encryption Library to have your wiki encrypted with 256 bit security.
Pro The equivalent of DataView/SQL already baked into the product
You can create lists of anything inside TiddlyWiki like tags, title structure, date, custom fields and present it as links, checkboxes, tables or whatever structure you need using a few lines of wikitext (a markdown-like language with powerful widget ability built-in).
Pro Stored in a single html file
The whole wiki, including all notes, is stored in a single html file.
Offline note taking often implies that you are travelling. In this case internet access is rare and your application needs to be mobile, i.e. you should be able to quickly put it on a usb stick. Because tiddlywiki runs in a single file, this is an easy task!
Pro Progressive user level, from ease of use to programming your own plugins
Basic users can start with simple note-taking, progressively discover predefined features and existing plugins, then start using more fancy features (like filters, widgets, macros), in order to adapt their wiki to their needs.
Pro Built in cloud saving for when one does connect to the internet
User can work offline as much as they want and once connected to the internet can then upload these changes with the built in cloud storage function called TiddlySpot. Other (non-built-in) solutions for cloud storage involve Google Drive, Dropbox, Github etc.
Cons
Con Does not work in all browsers
It does not work with the latest Firefox version anymore, due to the fact, that the Firefox security model changed. It needs third party tools to work correctly and to save things inside the file when edited through the browser.