This may seem ridiculously simple but it can help keep libraries organized and clutter-free:
Any time you put text in brackets into a to-do, it's a pretty good indicator that that text should really be a note to the to-do.
I have turned off new mail notifications and the badge on Mail.app that shows the number of unread e-mails. This prevents the rubber-neck reaction of getting an e-mail and stopping whatever task to look what it is. Instead, I schedule times to review my inbox and quickly scan through each e-mail to determine whether an action is associated with it. If so, I create a ToDo in Things, drag the e-mail to the Notes section of the ToDo and then file the e-mail out of the inbox. My goal at the end of the day is to have a clean inbox and a clean Today!