AnalogRead()

Can the Analog in ports be used in differential mode?

Doc

No. There is an analog comparator feature that can be used to compare AIN0 and AIN1 and generate an interrupt if AIN0>AIN1 but there doesn't seem to be a differential input mode (measuring the voltage difference between two pins). I think you have to measure the two pins relative to Ground and then calculate the difference.

I think you have to measure the two pins relative to Ground and then calculate the difference.

Yes that is correct. However you can use and external chip that has a differential input mode like in this project:-
http://www.thebox.myzen.co.uk/Hardware/Transistor_Tester.html

Cool chip, it's a shame it's 8bit... I did keep the datasheet and when I can, buy some on Ebay.
Thank You, Sir.
(Edit)
Check this one out...
http://cgi.ebay.com/ws/eBayISAPI.dll?ViewItem&item=261003564264#ht_3892wt_1163

Doc

The problem with differential ADC input is that to do it properly requires two ADC channels. The Atmel chip only has one, with an analog multiplex switch on the input to select the input pin (plus some internal sources).

Some chips that are arranged like this do have a pseudo-differencial mode, where they do two samples, one after the other, from different pins then subtracting one from the other, but this is no different to doing it in software.

Thank You that explains a lot, would have been useful for that power supply question in General Electronics.

Doc