The biggest giveaways are between the <head> </head>
tags.
Example WordPress head contents output by twentyten and how to remove:
<link rel="profile" href="http://gmpg.org/xfn/11" />
Remove directly from header.php
<link rel="stylesheet" type="text/css" media="all" href="http://example.com/wp-content/themes/twentyten/style.css" />
Change by calling your stylesheet from another location and or change the wp-content directory. Also your theme will need the commented information in style.css so it would be a good idea to call an alternate stylesheet.
<link rel="pingback" href="http://example.com/xmlrpc.php" />
Remove directly from header.php
<link rel="alternate" type="application/rss+xml" title="Example Blog » Feed" href="http://example.com/feed/" />
<link rel="alternate" type="application/rss+xml" title="Example Blog » Comments Feed" href="http://example.com/comments/feed/" />
<link rel="EditURI" type="application/rsd+xml" title="RSD" href="http://example.com/xmlrpc.php?rsd" />
<link rel="wlwmanifest" type="application/wlwmanifest+xml" href="http://example.com/wp-includes/wlwmanifest.xml" />
<link rel='index' title='Example Blog' href='http://example.com/' />
<meta name="generator" content="WordPress 3.1-alpha" />
To remove the extra links you can add a filter to functions.php
// remove junk from head
remove_action('wp_head', 'rsd_link');
remove_action('wp_head', 'wp_generator');
remove_action('wp_head', 'feed_links', 2);
remove_action('wp_head', 'index_rel_link');
remove_action('wp_head', 'wlwmanifest_link');
remove_action('wp_head', 'feed_links_extra', 3);
remove_action('wp_head', 'start_post_rel_link', 10, 0);
remove_action('wp_head', 'parent_post_rel_link', 10, 0);
remove_action('wp_head', 'adjacent_posts_rel_link', 10, 0);
You can change your plugin directory and your wp-content directory in your wp-config.php file but you could have some problems if your theme or any plugins are not written correctly.
define( 'WP_CONTENT_DIR', $_SERVER['DOCUMENT_ROOT'] . '/new-wp-content' );
Set WP_CONTENT_URL to the full URI of this directory (no trailing slash), e.g.
define( 'WP_CONTENT_URL', 'http://example/new-wp-content');
Optional
Set WP_PLUGIN_DIR to the full local path of this directory (no trailing slash), e.g.
define( 'WP_PLUGIN_DIR', $_SERVER['DOCUMENT_ROOT'] . '/new-wp-content/new-plugins' );
Set WP_PLUGIN_URL to the full URI of this directory (no trailing slash), e.g.
define( 'WP_PLUGIN_URL', 'http://example/new-wp-content/new-plugins');