Chrome/Firefox/Safari: Whether you're researching a new car purchase or a university paper, you're going to be dealing with a lot of different web pages. Annotary lets you highlight and mark up sites, save them for later, and even share your research with collaborators.
Annotary exists as a browser extension for Chrome, Safari and Firefox. Just invoke the app on a page you're using for research, and it will present you with a toolbox to save the page to your Annotary bookmarks and mark it up. You can highlight relevant blocks of text, and then type your own annotations into an on-screen sticky note. Once you're done, the page and all of your notes will be saved to your Annotary account, and you can even share the marked up page on social media or through email.
In concept, this is similar to the Evernote Web Clipper. However, I enjoy being able to make notes directly on the page itself, rather than just copying relevant passages to a separate app. Annotary is free, so give it a shot for your next research project.