Bookmark Tree - Web annotations Alternatives

Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, can be copied, tagged and modified either from the applications directly or from your own text editor.

Standard Notes is a simple and private notes app. It allows you to write and sync your notes across all your devices, including your iPhone, iPad, Mac, and web browser.

Evernote is a cross-platform, freemium app designed for note taking, organizing, and archiving.

A hierarchical note taking application, featuring rich text and syntax highlighting, storing data in a single xml or sqlite file.

Cryptee is a safety and privacy focused, encrypted and cross-platform personal data storage service. You can write personal documents, notes, journals, store photos and all sorts of other files.

Markup is an expert on web and document annotations. It allows you to highlight everything on PDFs, web pages, and ePub books. With Markup, you can easily add, manage, and back up your markups in one place.

Notezilla is the leading sticky notes app for Windows, Android, iPhone/iPad and the web. Set reminders to sticky notes, Pin sticky notes, attach them to websites, docs & folders, sync between PCs and other devices, organize using folders and tags.

Notejoy is a collaborative notes app for you and your team. It helps you get your most important work out of the noise of email & chat and into a fast and focused workspace.

Very similar to Notational Velocity but for Windows.

MemPad is a plain text outliner and note taking program with a tree structured index.