REST Server

• Restler, a PHP 5 RESTful API framework that makes that task sfupidly easy
• PHP.ActiveRecord 1.0 for easy database access (based on the proven Rails ActiveRecord pattern)
• Phinx for database migrations
• Codeception for BDD, using a tests-first approach
• PHP 5.4 for Traits and other awesomenesses
• MySQL for relational database structure
• « insert here server websocket library »

Admin client

• Ember for easy and sleek client UI
• jQuery 2.0

Reader clients

Mobile client

• Responsive layout to make the web client work in different devices
• After that, Titanium for complete mobile apps with a single, shared codebase
• « insert here mobile websocket library (will we use any?) »

Web client

• Same as the Admin client, plus:
• « insert here client websocket library »

Extensions

Chrome extension

Firefox extension

Composed by a main.js file that creates the needed toolbar button or menu entry, a panel (popup) if needed, and ties everything together. The panel is made of a complete HTML file that can include additional CSS and JS files if needed, so it's probably suitable to have it loading the original web reader.

Useful links:

• Popup sample with a widget button
• Altering pages based on URL matching
• Complete project of an annotator add-on, implementing hover behaviors over specific text elements
• Rikaichan, a Firefox add-on that implements hover definition on Japanese words. It was used to create the Rikaikun Chrome extension (Rikaikun code).

Adobe Reader plugin

This one depends on a totally different skill set, as the plugin should be created using C/C++ and the installation does not appear to be the most straight-forward (the user apparently needs to manually download the .api file and put it in the plugins folder). See the full documentation on Reader plugins.
Also, there's no documentation on plugins for Adobe Reader X yet, and it's not clear if plugins for version 9 are compatible, if there's still documentation to be released, or if custom plugins won't be supported anymore.