[More info added]. See below the code.

//~ change upload dir
add_filter(\'upload_dir\', \'choose_upload_dir\');

//~ upload image
$upload = wp_handle_upload( $_FILES[\'your_form_input_name\'], array(\'test_form\' => false) );

//~ change upload dir back
remove_filter(\'upload_dir\', \'choose_upload_dir\');

function choose_upload_dir($upload) {
    //~ your file to upload
    $file_type = $_FILES[\'your_form_input_name\'][\'type\'];

    //~ switch between file types
    switch($file_type) {
        //~ if type is \'png\' then upload subdir is \'/png\' and so on
        case \'image/png\':
            $type_dir = \'/png\';
        break;

        case \'image/jpeg\':
            $type_dir = \'/jpg\';
        break;

        default:
            $type_dir = \'/others\';
    }

    $upload[\'subdir\'] = $upload[\'subdir\'].$type_dir;
    $upload[\'path\'] = $upload[\'basedir\'].$upload[\'subdir\'];
    $upload[\'url\'] = $upload[\'baseurl\'].$upload[\'subdir\'];

    return $upload;
}
?>