In one app I wanted to have a panel to be updated automatically in 30 minute intervals.
You can run a javascript function in intervals with "window.setInterval()". That's the easy part.

But how to trigger a partial update to a panel/div from client javascript?

As always with XPages, it's a piece of cake once you know it: you can use XSP.partialRefreshPost(id) with the runtime id of that control to trigger the partial update.
You can even submit a piece of data with that function which you can get in the beforeRenderResponse event with something like:

Client side:
XSP.setSubmitValue(q);
XSP.partialRefreshPost(panelid);

Server side:
var map = facesContext.getExternalContext().getRequestParameterMap();
var values = map.get('$$xspsubmitvalue');

Thanks to Rocky Oliver, he pointed me to that technique in his session at Entwicklercamp 2010.