I am also having this problem. I updated from 2.x to 3.0.5 and comments stopped showing up. When I deactivate YARPP, everything is fine.
There are a bunch of messages like this one in my error_log:
[27-May-2009 15:16:56] WordPress database error You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '-1' at line 1 for query SELECT SQL_CALC_FOUND_ROWS wp_posts.*, yarpp.score FROM wp_posts join wp_yarpp_related_cache as yarpp using (ID) WHERE 1=1 AND wp_posts.post_type = 'post' AND (wp_posts.post_status = 'publish' OR wp_posts.post_status = 'private') ORDER BY wp_posts.post_date DESC limit -1 made by require, require_once, include, the_content, apply_filters, call_user_func_array, yarpp_default, yarpp_related, include, WP_Query->have_posts, do_action, call_user_func_array, Pager_hook, SEO_pager, query_posts, WP_Query->query, WP_Query->get_posts