Enclose code blocks within [code] shortcode, and let PHP and WordPress take care of the rest.

wp-code-shortcode.php

<?php


/*
 * Functionality to set up custom shortcode correctly.
 *
 * This function is attached to the 'the_content' filter hook.
 */
add_filter( 'the_content', 'run_bbcodes', 7 );
function run_bbcodes( $content ) {
	global $shortcode_tags;

	$orig_shortcode_tags = $shortcode_tags;
	$shortcode_tags = array();

	// Add custom shortcodes below
	add_shortcode( 'code', 'bbcode_code' );

	$content = do_shortcode( $content );
	$shortcode_tags = $orig_shortcode_tags;

	return $content;
}

/*
 * Allow code shortcode in comments
 *
 * This function is attached to the 'comments_template' filter hook.
 */
add_filter( 'comments_template', 'bbcode_in_comments' );
function bbcode_in_comments() {

	// Add custom shortcodes below
	add_shortcode( 'code', 'bbcode_code' );

	add_filter( 'comment_text', 'do_shortcode' );
}

/*
 * Add Custom shortcode functions below
 *
 * This function is attached to the 'sourcecode' shortcode hook.
 */
function bbcode_code( $atts, $content = null ) {

	// Ensure contents of a <pre>...</pre> HTML block aren't converted into paragraphs or line-breaks
	$content = clean_pre( $content );

	$content = str_replace(

		// Replace these special characters...
		array( '&', '<', '>', '\'', '"', '/', '[', ']', '\0' ),

		// ...with the HTML entities below, respectively
		array( '&amp;', '&lt;', '&gt;', '&apos;', '&quot;', '&#47;', '&#91;', '&#93;', '&#92;&#48;' ),

		$content
	);

	return '<pre><code>' . trim( $content ) . '</code></pre>';
}

/*

// ALTERNATIVE 'bbcode_code' function
function bbcode_code( $attr, $content = null ) {

	// Ensures that contents of a <pre>...</pre> HTML block aren't converted into paragraphs or line-breaks
	$content = clean_pre( $content );

	$content = str_replace(

		// Replace these special characters...
		array( '/', '[', ']', '\0' ),

		// ...with the HTML entities below, respectively
		array( '&#47;', '&#91;', '&#93;', '&#92;&#48;' ),

		// PHP function automatically replaces characters that have special significance in HTML (i.e. & < > ' ")
		htmlspecialchars( $content, ENT_QUOTES )
	);

	return '<pre><code>' . trim( $content ) . '</code></pre>';
}

*/

/*
 * Related sourcecode worth reading:
 *
 * https://bitbucket.org/cbavota/syntax-highlighter-plugin/src
 *
 * https://github.com/mdawaffe/Highlight.js-for-WordPress/blob/master/highlight-js.php
 *
 * https://github.com/fracek/highlight-wp/blob/master/highlight.php
 *
 * http://plugins.svn.wordpress.org/syntaxhighlighter/trunk/
 *
 * http://blog.webspace.jp/235
 */

?>