Currently, both are in use as the trade is in the middle of a 'phasing in' period that lasts until (as far as I know) around 2011/2012.
Older titles/editions will still have only 10-digit ISBNs, most current titles have both, and a few are now produced with just the 13-digit ISBN.
I would suggest that if you have both, then quote them. The database used by bulk suppliers and places like Amazon (plus most library systems) will currently accommodate both and, if you type in one, will automatically generate the other.
As Lie-in King advises, it's good to quote author and full title as well, because any ISBN only refers to one edition, which may not be available, although others are - and then the opportunity has been missed.