The one thing I have repeatedly learned in graduate school is that you will always be adding to your TODO list. This list is never ending and often bogs me down. Wunderlist works well for me because it allows me to set deadlines and has a friendly interface. I keep everything from school work to twitter post on it =)
If you have published a paper you should make a Google Scholar account. If you haven't published yet you should make a Google Scholar too! Google Scholar is like a Facebook for scientist, it allows others to easily find papers published by you and who you have collaborated with. It also recommends papers for you based on papers you have read and what you have published.
You are not always going to have time to take notes, sometimes you just want to jot something down quickly. This app allows users to take quick notes and find them easily in the future. Also it allows you to write (and preview) your notes in HTML and Markdown so that information can be easily be transferred to a website or maybe even a blog.
4) Dropbox/Google Drive
If you have not started using Dropbox or Google Docs yet, get on it! This allows you to access your information from any computer anywhere any time. That research paper you were putting off reading, put off no more. Another bonus to these services is that information is stored in the cloud, free backup. Although you do not ever think your computer will crash and 4 hours of work will be destroyed, it will happen, TRUST ME!