I have a site with over 3000 links that still struggles. I decided to research the strength of the links I was receiving. I ran a program to check the source code for each and it turns out that almost half of them have a rel=nofollow or rel=external nofollow in the linking code.
I checked many of the pages in question and they are just regular sites, articles and blogs linking in the regular way they always have. Only problem is, they seem to be too scared to link to anything anymore without nofollow in the link.
I emailed a dozen of them and only two responded. Both said they were aware that PR is still lost through the nofollow link. Both said "better safe than sorry" somewhere in the email.
Remind me ... how was this nofollow threat from Google supposed to help matters?