That is the same problem I was facing. I was using WordPress 3.0 built in widgets to add a category listing of categories I had created. The thing was that the categories I had created were for a Custom Post (content) Type that I had created myself using Custom Post Type UI plug-in that is so handy. The problem was that when I used the Category listing widget... although the listing of categories did show up... clicking on any single on of them took to me a 404 page on my own blog.
I took the code provided by parandroid and pasted in my functions.php file:
add_filter('pre_get_posts', 'query_post_type');
function query_post_type($query) {
if(is_category() || is_tag()) {
$post_type = get_query_var('post_type');
if($post_type)
$post_type = $post_type;
else
$post_type = array('post','<strong>cpt</strong><strong>'); // replace cpt to your custom post type
$query->set('post_type',$post_type);
return $query;
}
}
In the code above there is a variable "cpt". I simply replaced this variable, as instructed by parandroid, with the name of the Custom Post Type I had created (which in my case was "Advertisements") and voila... things worked perfectly.
Thanks for sharing. I am just posting this comment as I noticed no one had posted anything that would point to the succcessful implementation of the above.
If you have any questions or want any help doing any of the above mentioned, I'd be more than glad to help.
Khaled Hakim