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Does anyone know of a wysiwyg application for taking notes, preferably in a tree structure, which loads from and saves to HTML directly?

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Take a look at TiddlyWiki:

TiddlyWiki is a single html file which has all the characteristics of a wiki - including all of the content, the functionality (including editing, saving, tagging and searching) and the style sheet. Because it's a single file, it's very portable - you can email it, put it on a web server or share it via a USB stick.

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Perhaps Google Docs might suit you, it can be used offline if needed.

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Are you asking for an editor to embed into your Web page, or to use as a desktop tool?

If it's the latter, I'd suggest picking the tool you are most comfortable with. I'm a big fan of TiddlyWiki, but you may wish to have something that runs as a native app instead. Almost all the current note taking and mind mapping programs out there have an HTML export option (see http://en.wikipedia.org/wiki/Comparison_of_notetaking_software). And if all you need is a basic bullet list, there are plenty of good HTML editors like Amaya, CoffeeCup and BlueFish.

On the other hand, if what you are after is a way to take notes directly on a web page or web application, the editor component I'd recommend is TinyMCE. There was a recent review of the top 25 editors on Smashing Magazine, check it out for a good overview.

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