My current work is working on one single website, so it's just one long project really :) I actually don't have deadlines, so it's kind of weird to work here. It's hard to push yourself for a personal deadline if there are no consequences.
I don't have a really organized way of doing things. I basically break a 'project' (for me that's HTML/CSS/JS, mostly templating/designing) down into smaller parts. I tend to start with the overall layout (header, main, footer) and work my way from top to bottom mostly. So to-do lists usually do the trick ;)
Since I'm designing via code, I tend to re-iterate multiple times. Sometimes things that I think out just don't work out or are crap UX/UI wise and then I start over and start sketching on paper again, haha.
I reckon that developers in Agile/SCRUM teams will have a way more structured approach than I have, so I think it will be more interesting to see what tools they use.