I found out that the site I was working on was still using PHP 4.4, something like that. I upgraded it to PHP 5.2, and the Warning goes away. Everyone is going to have to upgrade to PHP 5.2 in order to run 3.2, so this issue presumably will become moot really fast.
I’m in the same situation as bobcouttie – on just my pages I am receiving the warning in regards to this warning. I’m using WP 3.1.3.
Notice: Only variables should be assigned by reference in /<removed>/wp-includes/query.php on line 1600
