Rohan Kshirsagar has a nice post on integrating Emacs Org Mode into the software engineering process. That's a big subject area, of course, but Kshirsagar focuses on using Org to take notes as things occur to you and perhaps turn some of them into TODO items. That's only a tiny bit of the Org functionality that can be useful to a developer but it's an important one.
The idea is that as you're working some idea may occur to you and you'd like to capture it. If you have to switch to another application and do a lot of busy work to write your idea down, you can lose focus on your main task. A nice thing about Org is that it has a built-in facility to quickly and easily capture notes and store them in an Org file. It doesn't take many brain cycles because almost everything is automatic.
I like this facility so much that I even have a global hot key to bring up the Org capture menu from any application on my machine. I mostly use this in conjunction with the browser when I want to make a note of something I'm reading but it works from anywhere.
Kshirsagar also points out that if—heaven forfend—some members of your team are not Emacs users, Org mode makes it easy to publish the notes as HTML and share them either on the team server or a public area of your workstation. It's a useful post and worth a read so head on over.