Site-wide links with the same textual pattern (i.e same anchor text, positioning etc.) from relevant sites are discounted, but no more than those site-wides that are acquired from non-relevant sites. They won't harm or else I will be getting them for my competitors.
I can't really say I have settled on a solid position on this subject. But I have noticed that on my cities directories I have more traffic to those pages on which I have relevant sitewide backlinks. For example I started a statewide cities directory for my home state ( 640 or so main city pages )after it achieved a lil' PR I then started a countrywide cities directory ( 42,572 city pages ). Naturally on each city page of the state site I placed a link to the co-responding city page on the larger countrywide site. To this day the cities in home state recieve ten times the search engine traffic as the other states combined.... I think this is a good indication that under these conditions ( relevancy ) the site wide links are no doubt beneficial... I do however agree that usually under ordinary conditions a single link from a unique domain ( preferably unique ip block as well ) is a better value and that sitewide links are not given the same weight as a unique relevant link.