Recently I found two websites that can be used to organize your thoughts. They provide a space for you to put your entire brain in one place. The first one is called Workflowy. It is a giant page, which is completely blank when you first start. You can then create bullet points and click on the bullet points to create a folder of sorts, and place more bullet points inside of that. This way, you create a hierarchy of lists. So, when I was using it, I had a list for school, graduate school, writing ideas, goals, and a few others I can't remember.
As a free member, you are allowed to to create five hundred items per month. If you sign up using this link: Sign up for Workflowy, you and I both get an extra 250 items per month. I'm doing this more for your benefit than mine since I no longer use Workflowy. I now use Trello, which I will talk about in the next paragraph.
Trello is another website that allows you to organize all of your thoughts in one place. Instead of using one page, with a bunch of bullet points that can act as folders, Trello uses boards. Boards are like folders, and inside of them are lists, which contain cards. Again, it's a nice hierarchy, although it looks and feels quite different from Workflowy. I like Trello more for a few reasons. First of all, it has a more appealing interface (I'm a sucker for good looking applications). However, that alone was not enough to make me switch since I also enjoy minimalist applications (Workflowy is more minimalist). The deciding factor for me was that Trello allows you to add images, checklists, links, and more. Overall, these added features make it a stronger and more useful site in my opinion. Here is the link, although I don't think we get anything from this one except the opportunity to organize our brains: Sign up for Trello.
Which one is right for you? That's completely a matter of personal preference. I've used both websites, and they both work well for organizing your thoughts and ideas. My advice is that you sign up for both (neither of them spam you) and see which one you prefer. If you do sign up and find you like one more, leave me a comment and tell me which one, or if there's an even better site, let me know.
Update (2015): I no longer use Workflowy or Trello. Instead, I organize all of my thoughts using a system of folders and documents in DropBox. This is more convenient to me because it is all located on my computer and doesn't seem as gimmicky.