uploads.php

// put uploaded files into filetype based directories

add_filter('wp_handle_upload_prefilter', 'wpse_25894_handle_upload_prefilter');
add_filter('wp_handle_upload', 'wpse_25894_handle_upload');

function wpse_25894_handle_upload_prefilter( $file )
{
    add_filter('upload_dir', 'wpse_25894_custom_upload_dir');
    return $file;
}

function wpse_25894_handle_upload( $fileinfo )
{
    remove_filter('upload_dir', 'wpse_25894_custom_upload_dir');
    return $fileinfo;
}

function wpse_25894_custom_upload_dir($path)
{   
    // Determines if uploading from inside a post/page/cpt
    // If not, default Upload folder is used
    $use_default_dir = (
            isset($_REQUEST['post_id'] ) 
            && $_REQUEST['post_id'] == 0 
            ) 
            ? true : false; 

    if( !empty( $path['error'] ) || $use_default_dir )
        return $path; //error or uploading not from a post/page/cpt 

     // Save uploads in FILETYPE based folders. When using this method, 
     // you may want to change the check for $use_default_dir
     $extension = substr( strrchr( $_POST['name'], '.' ), 1 );

     switch( $extension )
     {
        case 'jpg':
        case 'jpeg':
        case 'png':
        case 'gif':
            $customdir = '/images';
            break;

        case 'mp4':
        case 'm4v':
            $customdir = '/video';
            break;

        case 'mp3':       
            $customdir = '/audio';
            break;

        case 'txt':
        case 'doc':
        case 'pdf':
            $customdir = '/documents';
            break;

        default:
            $customdir = '/otherfiles';
            break;
     }

    //remove default subdir (year/month)
    $path['path']    = str_replace($path['subdir'], '', $path['path']); 
    $path['url']     = str_replace($path['subdir'], '', $path['url']);  

    $path['subdir']  = $customdir;
    $path['path']   .= $customdir; 
    $path['url']    .= $customdir;  

    return $path;
}