OK I have set up a new site recently and I'm having a blast with link build atm getting PR5+ dofollow .edu .gov links. I recently hit a spam filter for http://example.com so I started using http://www.example.com My question is which one is better? I have the www. 301 redirecting to my site root and my site displays as the site root in google, will these links even show up? I know the PR passes, but I can recall the links for different extensions being indexed differently??? If I just built all of my links to www. would that be OK? EDIT: sorry I am asking this in a ranking perspective, will my site (rootdomain) rank for the anchors keywords I build for the top level domain?
I think The best link you can build is from a related site, then links from authority websites is more valuable. One-way links are considered to be natural links and not an attempt to manipulate rankings.
Are you sure that the spam filter recognizes www.example.com and example.com as two different domains?
You won't get rid of the Google's penalty by removing the www part. Try to find out why your site was penalized, fix the problem and get it reviewed by the Google staff.
Just send an email to the google staff sking for an expanation. Change whatever they say and let them know you did so. It may take a little but it will work.