Annotate your email with Chrome extension Gmail Notes
Once you sign in, the extension icon in your Omnibar will display a small, green dot to let you know it's ready to store your notes. When you're on a conversation which warrants a note, simply click the icon and enter your text into the pop-up and click save. You're limited to one note per message at the moment, but it's still a handy way to add a reminder to your conversations.
They're saved into your Google Docs storage, so you can access your raw notes from there as well. They're not very useful without the context of your Gmail conversation of course, but it's certainly a logical place to store the data.