I'll have a think Bashy as I'm sure there is another way of doing it.
(BTW, I'm staff now :))
Ok here we go
search.php?do=getnew&exclude=X,Y
Replace the X and Y with the forumid numbers that you wish to exclude from your search. You can add more id's by just seperating them with commas.
To add this to your current navbar
find
<td class="vbmenu_control"><a href="search.php?$session[sessionurl]do=getnew" accesskey="2">$vbphrase[new_posts_nav]</a></td>
replace with
<td id="navbar_search_new" class="vbmenu_control"><a href="search.php?$session[sessionurl_q]do=getnew&exclude=X,Y" accesskey="4" rel="nofollow">$vbphrase[new_posts_nav]</a> <script type="text/javascript"> vbmenu_register("navbar_search_new"); </script></td>
making sure you make the X and Y replacements.
find
<!-- header quick search form -->
<div class="vbmenu_popup" id="navbar_search_menu" style="display:none">
above add
<div class="vbmenu_popup" id="navbar_search_new_menu" style="display:none">
<table cellpadding="4" cellspacing="1" border="0">
<tr>
<td class="vbmenu_popup"><a href="search.php?$session[sessionurl_q]do=getnew&exclude=X,Y" accesskey="4" rel="nofollow">Limited Search</a></td>
</tr>
<tr>
<td class="vbmenu_popup"><a href="search.php?$session[sessionurl_q]do=getnew" accesskey="4" rel="nofollow">$vbphrase[new_posts_nav]</a></td>
</tr>
</table>
</div>