To-Do List: Wunderlist - A free app which runs on all platforms (Windows, Mac, Android, iPhone) and the web. The program syncs across multiple devices and provides notifications, due dates, and reminders. More information
Note-taking: Evernote - A free app that syncs across multiple platforms. The program is based on creating electronic "notebooks" in which the "note" pages can include text, PDF files, text clips from websites and audio clips. Notes can be shared, tagged, and notated by a group. Many youtube videos and blogs have been written on how to use Evernote to manage research projects.
Bookmarking: Pocket - Free app can now be integrated into all browsers. Program allows you to save articles, videos, images, text, and links direct from the browser or other apps like Twitter, Flipboard, and Instagram. Resultant files can be read offline.