AddDefaultCharset utf-8
php_flag magic_quotes_gpc Off
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_URI} !^/template/img/favicon.png 
RewriteCond %{REQUEST_FILENAME} !-f  
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?module=$1 [L,QSA]

http://site.ru/messages/?pm=1

messages/

messages/?pm=1

RewriteBase /

хотя должно:
messages/?pm=1

array (size=2)
  'module' => string 'messages/' (length=9)
  'pm' => string '1' (length=1)

AddDefaultCharset utf-8
php_flag magic_quotes_gpc Off
RewriteEngine On
#RewriteBase /
RewriteCond %{REQUEST_URI} !^/template/img/favicon.png 
RewriteCond %{REQUEST_FILENAME} !-f  
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?module=$1 [L,QSA]

<?php
 var_dump($_GET);