I ran into the problem of people linking to a site using both
www.example.com
and
example.com

Since SE's see this as two different pages, we 'forwarded' example.com to www.example.com using a 301 redirect in a .htaccess file. Which means... we told the SE bot that example.com was permenantly moving to www.example.com.

This had the effect of combining our SE rankings. Now, only www.example.com links show in the SERP's.

Take a look at slashdot.org. if you type www.slashdot.org, it turns into slashdot.org (in the address bar).. It's a nice trick I do on every website i work with now.

Brett