Ranked in these QuestionsQuestion Ranking
Pro Open Source
Hypothesis is completely free and open source, its source code is hosted in GitHub.
Pro Chrome browser extension
Has browser extension for Chrome, which makes the job of annotating web pages even easier.
Pro Everything can be searched through
Searchable stream of annotations, replies, and email notifications.
Pro Private or public
You can work in private groups and then publish, keep annotations private, or make it public from scratch.
Pro Unique URLs for each annotation
You can link directly to an annotation.
You can sort by tags, which makes it far more powerful.
Con No browser extensions apart from Chrome
Allegedly, one can use bookmarklet instead, but in Firefox it works only for some of websites.
Con Seems under development
Too many rough edges and/or bugs as you use it. For example, you have to keep logging in every time you want to add a page using the chrome extension. There are ways to add annotations on the mobile too, but way too buggy. Hopefully they fix these problems soon. Very good idea; poorly implemented.