Example Custom Post Type and Custom Taxonomies.

<?php
/*
Plugin Name: Custom Post Type Test
Plugin URI: http://zed1.com/
Description: Testing Custom Post Types in WordPres 3.3
Author: Mike Little
Version: 0.1.0
Author URI: http://zed1.com/
License: GPLv2 or later
*/

new cpt(); // kick it all off

class cpt {
    function __construct() {
        register_activation_hook( __FILE__, array( 'cpt', 'activation' ) );
        register_deactivation_hook( __FILE__, array( 'cpt', 'deactivation' ) );
        add_action( 'init', array( 'cpt', 'init' ) );
        add_filter( 'the_content', array( 'cpt', 'extra_content' ) );
    } // end constructor

    static function activation() {
        self::register_cpt();
        self::register_taxes();
        self::flush_rules();
    } // end activation

    static function deactivation() {
        self::flush_rules();
    } // end deactivation

    static function flush_rules() {
        flush_rewrite_rules();
    } // end deactivation

    static function init() {
        self::register_cpt();
        self::register_taxes();
    } // end init

    static function register_cpt() {
        if ( !post_type_exists( 'cpt' ) ) {
            $labels = array( 'name' => _x( 'CPTs', 'post type general name' ),
                             'singular_name' => _x( 'CPT', 'post type singular name' ),
                             'add_new' => _x( 'New CPT', 'add new singular name' ),
                             'add_new_item' => __( 'Add New CPT' ),
                             'edit_item' => __( 'Edit CPT' ),
                             'new_item' => __( 'New CPT' ),
                             'view_item' => __( 'View CPT' ),
                             'search_items' => __( 'Search CPTs' ),
                             'not_found' =>  __( 'No CPTs Found' ),
                             'not_found_in_trash' => __( 'No CPTs found in Trash' ),
                             'parent_item_colon' => '-:-'
                           );
            $args = array( 'labels' => $labels,
                           'public' => true,
                           'publicly_queryable' => true,
                           'show_ui' => true,
                           'query_var' => true,
                           'rewrite' => true,
                           'has_archive' => 'cpts',
                           'capability_type' => 'post',
                           'hierarchical' => true,
                           'show_in_nav_menus' => true,
                           'menu_position' => 100, // last block
                           'supports' => array( 'title',
                                                'editor',
                                                'excerpt',
                                                'comments',
                                                'revisions',
                                                'page-attributes',
                                                'shortlink' )
                         );
            register_post_type( 'cpt', $args );
        }
    } // end register_cpt

    static function register_taxes() {

        if ( !taxonomy_exists( 'tax1' ) ) {
            $tax_labels = array(
                                'name' => _x( 'Taxonomy ones', 'taxonomy general name' ), // there will only be one
                                'singular_name' => _x( 'Taxonomy one', 'taxonomy singular name' ),
                                'search_items' =>  __( 'Search Taxonomy ones', 'dmd_school' ),
                                'popular_items' => __( 'Popular Taxonomy ones', 'dmd_school' ),
                                'all_items' => __( 'All Taxonomy ones', 'dmd_school' ),
                                'parent_item' => null,
                                'parent_item_colon' => null,
                                'edit_item' => __( 'Edit Taxonomy one', 'dmd_school' ),
                                'update_item' => __( 'Update Taxonomy one', 'dmd_school' ),
                                'add_new_item' => __( 'Add New Taxonomy one', 'dmd_school' ),
                                'new_item_name' => __( 'New Taxonomy one Name', 'dmd_school' ),
                                'separate_items_with_commas' => __( 'Separate Taxonomy ones with commas', 'dmd_school' ),
                                'add_or_remove_items' => __( 'Add or remove Taxonomy ones', 'dmd_school' ),
                                'choose_from_most_used' => __( 'Choose from the most used Taxonomy ones', 'dmd_school' )
                               );

            register_taxonomy( 'tax1', 'cpt', array(
                'hierarchical' => false,
                'labels' => $tax_labels,
                'show_ui' => true,
                'query_var' => true,
                'rewrite' => array( 'slug' => 'tax1s' ),
                ) );

            // add some predefined ones
            if ( get_term_by( 'slug', 'tax1-term1', 'tax1' ) === false )
                wp_insert_term( 'Tax One term one', 'tax1', array( 'slug' => 'tax1-term1', 'description' => 'Term number one for taxonomy one' ) );

        } // end if tax ! exists

        if ( !taxonomy_exists( 'tax2' ) ) {
            $tax_labels = array(
                                'name' => _x( 'Taxonomy twos', 'taxonomy general name' ),
                                'singular_name' => _x( 'Taxonomy two', 'taxonomy singular name' ),
                                'search_items' =>  __( 'Search Taxonomy twos', 'dmd_school' ),
                                'popular_items' => __( 'Popular Taxonomy twos', 'dmd_school' ),
                                'all_items' => __( 'All Taxonomy twos', 'dmd_school' ),
                                'parent_item' => null,
                                'parent_item_colon' => null,
                                'edit_item' => __( 'Edit Taxonomy two', 'dmd_school' ),
                                'update_item' => __( 'Update Taxonomy two', 'dmd_school' ),
                                'add_new_item' => __( 'Add New Taxonomy two', 'dmd_school' ),
                                'new_item_name' => __( 'New Taxonomy two Name', 'dmd_school' ),
                                'separate_items_with_commas' => __( 'Separate Taxonomy twos with commas', 'dmd_school' ),
                                'add_or_remove_items' => __( 'Add or remove Taxonomy twos', 'dmd_school' ),
                                'choose_from_most_used' => __( 'Choose from the most used Taxonomy twos', 'dmd_school' )
                               );

            register_taxonomy( 'tax2', 'cpt', array(
                'hierarchical' => true,
                'labels' => $tax_labels,
                'show_ui' => true,
                'query_var' => true,
                'rewrite' => array( 'slug' => 'tax2s' ),
                ) );

            // add some predefined ones
            if ( get_term_by( 'slug', 'tax2-term1', 'tax2' ) === false ) {
                wp_insert_term( 'Tax two term one', 'tax2', array( 'slug' => 'tax2-term1', 'description' => 'Term number one for tax two' ) );
            }
            if ( get_term_by( 'slug', 'tax2-sub-term2', 'tax2' ) === false ) {
                $term = get_term_by( 'slug', 'tax2-term1', 'tax2' );
                wp_insert_term( 'Tax two sub term two', 'tax2', array( 'slug' => 'tax2-sub-term2', 'parent' => $term->term_id, 'description' => 'Sub Term number two for tax two' ) );
            }
        } // end if tax ! exists

    } // end register_taxes

    static function extra_content($content) {
        return $content
                . get_the_term_list( $post->ID, 'tax1', 'Tax One: ', ', ' , '' )
                . get_the_term_list( $post->ID, 'tax2', 'Tax Two: ', ', ', '' );
    } //end extra_content

} // end class cpt

/* put this in your side bar
<?php list_cpts(); ?>
*/

function list_cpts( $args = array() ) {
    global $post;
    $default_args = array( 'post_type'=>'cpt', 'title_li'=> __('CPTs') );

    if ( is_single() && ( 'cpt' == $post->post_type ) ) {
        if ( $parent_id = wp_get_post_parent_id( $post->ID ) ) {
            $default_args['child_of'] = $parent_id; // get siblings
        } else {
            $default_args['child_of'] = $post->ID; // get children
        }
    }

    $args = array_merge( $default_args, $args );
    return wp_list_pages( $args );
}