I always thought Google understands a site-wide link does not equal to sending thousands of links to the same website...
In terms of linking credit, this is true... ie, Google is not going to give a site receiving thousands of sitewide links from one domain thousands of links worth of credit. Some say the credit from a run-of-site link is closer to one link, and some say the credit might not help rankings at all.
Sitewides often can be a sign of coordination between sites, though, and in that regard they can hurt you.
Depending on the link profiles of the linking and receiving sites, on the quality of inbound links, the temporal patterns of link acquisition, anchor text, excessive interlinking or other signs of link coordination... Google might hold these links against the linking site, or the receiving site, or both.
If the sites involved have strong, "natural" link profiles and have established a high level of trust with Google, an occasional inbound blogroll link might not hurt, but I'd rather not have them. I assume that the linking site carries more responsibility for a link than the receiving site. Run-of-site links from large sites that are not blogs, IMO, are probably much more suspect than blogroll links. I've long thought that ROS links are completely unnatural.