Testing for Production

Can someone give me some ideas on ways and means to design in test points (or other test tools) on a board for production.

What should I try and focus on while running post assembly tests? Functionality or electrical connectivity?

My board is battery operated with a single micro. Any functional tests would have to first burn in the flash before it can work.

I am a little skeptical about only electrical testing, since the manufacturing processes are all automated anyway, should I even consider the possibility of one off boards having problems? I mean is yeild really a factor to consider?

Also any ideas on how to make a low cost jig for testing small quantities inhouse.

You might want to try asking this on one of the usenet newsgroups (sci.electronics.design, or comp.arch.embedded, maybe). There are some trolls and flamers, but there are also a lot of people who do this professionally and are happy to offer advice.