During the research phase of any writing work, ideas for your arguments, examples and illustrations can literally come from anywhere. It's not uncommon to pick up one or two ideas each from several books, websites, magazines, journals and all sorts of secondary sources.
Grabbing a hold of these things when you're writing is not easy. Without you have eidetic memory, you'll likely forget more of them than you'll remember. As such, gathering these individual nuggets into a single source, where you can refer to them handily, is an important part of streamlining your work process into something better and more efficient.
There are many ways you can organize these sources.
1. An idea notebook. Whether you use a physical notebook or a software-based electronic one, having a single place where you can take down ideas, thoughts and research gives you an easy-to-access facility that you can use when you need to refer to them later. In case you're searching for good notebook software for writing, the most popular at the moment are Microsoft's OneNote and Evernote, with the latter having the advantage of supporting numerous mobile platforms, including Android, iPad and iPhone.
2. Mind maps. A diagram intended to show relationships between different ideas, this is my preferred method of organizing information. Not only does it let you keep all research for a topic in a single place, it allows you to show relationships between them in a visual, easy-to-understand manner.
3. Index cards. Similar to using a notebook, you jot notes down on index cards that you keep in your pocket. This makes it easy to get rid of individual items (just throw them away) or add new ones, all while having all the information right in your pocket.