Windows only: Screen capture tool Screenpresso takes screenshots of part of your screen, a specific window, or the whole screen with a shortcut key, then lets you edit, add effects, and even share with email or Twitter.
Windows: If you're a fan of the web site monitoring service Pingdom, they've released a handy desktop alert app to put site updates in your system tray. After going public earlier this year, Pingdom offered free single-site monitoring including SMS alerts, email alerts, and an iPhone app. Now you can grab a free account and the Pingdom Desktop Notifier for instant system-tray confirmation that your monitored site is online and functioning.
Windows/Mac/Linux (with Adobe AIR): Note-taking application Scribbly lives in your system tray and lets you quickly write notes or reminders to yourself, and then will email them to you with a single click.
Windows only: Firefox extension MinimizeToTray Revived is a replacement for the popular MinimizeToTray extension (which has since been abandoned and doesn't support Firefox 3 or later). The simple extension puts Firefox in your system tray with a click of your mouse or a keystroke.