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Autism Timer is a digital timer that shows the elapsed time clearly and is easy to use. You can set three different time for green/yellow/red zone. When the timer is done, it beeps/vibrate and show the black and white square flag. It uses the full screen of the iPhone/iPod touch without any additional clutter while running.

Focus:  Set Specific Tasks that you're working on with a timer and then do them. 

a visual timer for Windows. Free download, gradually reveals an image. free images and sounds You can probably download to a usb stick and then install on unmanaged computers. I have not tried to make it appear under a student or teacher log in

30/30 app helps you set a timer for the different parts of your day. Could students use this as a way to organize themselves when doing homework?

online=stopwatch.com stop watch or count down clock

Due is a very simplistic reminder app but expensive at $4.99. It does synch via drop box or the icould