Ping, ping, ping. Software should stay out of the way so I can get stuff done.
I have trouble focusing on some types of tasks and need to turn notifications off and use alarms and timers to stay on task. I've written about my constant pursuit of focus. To give you an idea of how obsessive I am about this, take a look at what my desktop looks like. These are some of the apps I use to put the blinders on. This list was originally maintained at Bagcheck.
Notational Velocity is my do-it-all notebook. It functions as my commonplace book and stores ideas and notes I want to recall later. I love this tool above all other note-taking tools because it's a minimal text editor with virtually no interface--the flow from launch to search/open or create/edit is a seamless text-only experience.
It syncs with Simplenote, so I can access/edit on my iPhone and iPad. The nvALT fork lets me use Markdown when I want to start a web page or blog entry draft, and exports the content as valid HTML.
I love the simplicity of the iA Writer and that is has some simple text formatting using Markdown. The focus mode is nice, although I rarely use it. Uses Markdown and can sync with DropBox and the iPad version. See also OmmWriter
I use Mailplane so I never have to have a Gmail window open in a browser tab. I can turn notifications on and off, switch between email accounts, and drag and drop attachments into messages. Best of all, it feels more like a single-purpose mail app than a web app.
Quicksilver was my launcher for years. Alfred has replaced it. Minimal and there when I need it, and does much more than I expect it to.
This is an unobtrusive Pomodoro timer that sits in the menubar so you can set it when you start a task. The Pomodoro Technique uses 25 minute increments for focusing on tasks.
I'm a single-application mode Mac user. I use Cmd-Opt-Click to view apps in single app mode, so when I do, I like to position app windows front and center, or sometimes pinned to one side or expanded to full screen. Divvy lets me click Cmd-Shift-Space to do this in a split second.