Anytime I get a chance, I try to use the productivity applications. These may be associated with time management or structuring ideas etc. I found out that there is no best way to do this. Every application has some heuristics behind, and these are mostly decided by the developers. Sometimes an app may seem to solve your problem, but later you may realize that it is not what you want or need. In my opinion, **you need to come up with your own way to do it**. However, let me list some ways/advices I encounter:

 - Open a google document. Write down your ideas as a list. If you need
   to structure them, nest the list items. Go over the document
   periodically.
 - Take a look at [wunderlist][1]. They have done a good
   job task/note management. [wunderlist 2][2] has just released with new features.
 - [Trello][3] is another example. It may seem
   to be an project management tool, but you can use for managing your
   ideas on a whiteboard-style.
 - [Springpad][4] is another way to    save/organize things online.
 - Your example [Evernote][5], and others    like [do.com][6],
   [todoist][7] can be listed also. If you really need    to find the
   right application you need to search hard. Take a look at [here][8] as well.
 - [Mindmup][9] is a online mind mapping tool.
 - [Hiro][10] is another newly released tool. Try it [here][11].

For me, the best way is to keep a small notebook and write down what I have done in terms of research day by day. I also note the ideas for my thesis. After some point, when you go back and check your progress, you would be amazed how much things changed and become more mature. But the most important thing is that I realized what is best for me is to grep a pen and write down it on a paper rather than some website.


  [1]: http://www.6wunderkinder.com/wunderlist
  [2]: http://www.6wunderkinder.com/wunderlist
  [3]: https://trello.com
  [4]: http://springpad.com
  [5]: http://evernote.com
  [6]: https://do.com
  [7]: http://todoist.com
  [8]: http://alternativeto.net/software/evernote/
  [9]: http://www.mindmup.com/
  [10]: https://www.hiroapp.com
  [11]: https://alpha.hiroapp.com