I second the Gymboss timer. I used it when I first started running and it's very simple and inexpensive. Find it here: www.gymboss.com/
You can set up two different time intervals, for example 5 minutes and 2 minutes. Then you can set it to beep, vibrate or both at the end of the interval. So, you could run for 5 minutes, it'll beep, you walk for 2 minutes, it'll beep again, and you run again for 5 minutes...or whatever your program is.
I'm using the Nike Plus for ipod now. It's nice because it keeps track of time, distance, calories, pace, and you can still listen to whatever music you like. Sometimes I find the distance isn't entirely accurate, but I'm not picky.
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