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(Linux-Ubuntu Maverick 10.10)
I tried Workrave and it was alright but took up a lot of space in the systray and felt clunky, sort of stressed me. You might be able to change some of this with different settings but I still couldn't imagine using it all day.
RSIBreak is a wonderful alternative. Streamline, with only one icon in the systray that shows the countdown/intervals as a pie chart . Lets you choose how to be alerted, whether it notices when you go idle, adjustment for tiny breaks and long breaks, temporary suspend, usage statistics. Has it all right in your tray but not at all clunky or complicated way.
It is a KDE app but it is working wonderfully in Ubuntu and can be found in the repository.
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