It doesn't make any difference UNLESS you have links coming into the site that use different variations of the domain (
www.domain.com and domain.com).
Both of those are different websites and se spiders will treat them as such. So if you have nn links coming into
www.domain.com, and the internal links are relative, then se spiders will crawl the pages as being relative to
www.domain.com. But if you have one or two links coming into domain.com, and the internal links are relative, the internal pages will be crawled as being relative to domain.com. The result is that the PageRank that the domain.com IBLs should have brought into the site is spread between the pages on a different site - domain.com.
Did I write that in an understandable way?