ExpressionEngine has a plugin that you can use to wrap comments and trackbacks so all links in them have the rel=“nofollow” attribute. Information on the attribute can be found at this Google entry.
You can find it at the pluginssite. This is the example code, taken from there:
[code]
{if author_id == '0'}
{exp:no_follow whitelist="y"}
{comment}
{/exp:no_follow}
{/if}
{if author_id != '0'}
{comment}
{/if}