How do you take notes on a computer?

I'm wondering if there's anything easier than using Google Docs to take notes. I considered using different Docs files for each book, but I don't want that many files. I can use one for every single book, and I have to go through the trouble of bolds and italics and formatting. The only reason I don't use paper is because it deteriorates and sometimes gets lost.

For those who take notes on what you're reading, what do you use?