If you are managing the websites via Google Webmaster Tools, it is possible to specify the "primary domain".
However, the world of search engines doesn't stop with Google, so your best bet is to send a 301 redirect to your primary domain. For example.
www.foo.net should 301 redirect to www.foo.com
www.foo.net/bar should 301 redirect to www.foo.com/bar
and so on.
This will ensure that www.foo.com gets the entire score, rather than (potentially) a third of the score that you might get for link-backs (internal and external).