I had the same issue that was raised here: http://drupal.org/node/1040196 and solved it by writing a small module that defines a new formatter for the node_reference field type. It allows you to select a field to be displayed instead of title, defaulting to title when no data exists in that field.
At the moment it is rather crude, since it selects 'value' with a delta of 0, so it won't work for fields that do not use the 'value' key when storing data and will always return the first value only. Still, it will work in most cases, and it's still a work in progress. Comments and reviews are welcome, especially from those more familiar with drupal.