[tomjen3]

Having used it extensively, you can setup org-mode however you want: a file per month, a file per thought, a file per project and everything in between.

It is also the only note taking system I have seen that will let you link to an email. If you want to add a todo entry deep in some meeting notes reminding you to checkup on that email in 3 weeks, you can. And those todos will then show up in your agenda view.

Unfortunately this doesn't work if you don't already use Emacs as your email client, which I guess you don't if you aren't also using org-mode.