Forgot to use l() for the taxonomy links.

themes/goofy/goofy.theme

@@ -120,7 +120,7 @@ function node($node, $main = 0) {
         if ($terms = taxonomy_node_get_terms($node->nid)) {
           $taxlinks = array();
           foreach ($terms as $term) {
-            $taxlinks[] = "<a href=\"index.php?or=$term->tid\">". check_output($term->name) ."</a>";
+            $taxlinks[] = l($term->name, array("or" => $term->tid), "index");
           }
           $subright = $this->links($taxlinks);
         }

themes/unconed/unconed.theme

@@ -105,7 +105,7 @@ function node($node, $main = 0) {
               if ($terms = taxonomy_node_get_terms($node->nid)) {
                 $taxlinks = array();
                 foreach ($terms as $term) {
-                  $taxlinks[] = "<a href=\"index.php?or=$term->tid\">". check_output($term->name) ."</a>";
+                  $taxlinks[] = l($term->name, array("or" => $term->tid), "index");
                 }
                 $taxo = $this->links($taxlinks);
               }