A research notebook is just a place to document your ideas. It can be a phyiscal notebook, a folder on your computer, a blog, or anything you want.

The format of your research notebook is personal. There are infinitely many possibilities; what matters is that you choose a format and workflow that work for you. To be honest, most of us are constantly updating and refining our workflow. So think about what will be useful and functional for you right now... and then put just enough time into thinking about it to get moving. You can always migrate content if needed!

Some considerations:

Public/private: it's great to have a public blog to document things, but often it helps to have somewhere that you can channel your thinking directly without worrying about editing, privacy, etc. On the other hand, if you ultimately want to share your thinking and can go straight to an informal blog post, then it's less work overall. 

Tagging: tagging is helpful to indentify recurring themes and interests. Some kind of search mechanism also helps you go back in time. 

Overhead: ideally you want something that is low overhead, so that within moments of having an idea you can be writing it down or otherwise documenting it. 

Examples: moleskin, spiral bound notebook from college bookstore, wordpress (private or public), jekyll/octopress (static blogging), directory of text files, mediawiki... add your examples to the comments. 

Todo: post a comment describing the format of your research notebook, and any tips/ideas that might help others. If you can, include a URL, screenshot, or image of your analog notebook.