A simple proof-of-concept plugin to hide specific plugins from Plugins' list in WP Admin if it is a Multisite install and the user is not the Super Administrator.

arunas-hides-plugins.php

<?php
/*
Plugin Name: Arunas Hides Plugins
Plugin URI: http://arunas.co/hidesplugins
Description: A simple proof-of-concept plugin to hide specific plugins from Plugins' list in WP Admin if it is a Multisite install and the user is not the Super Administrator.
Author: Arūnas Liuiza
Version: 0.2
Author URI: http://arunas.co/
*/

add_filter('all_plugins', array( 'ArunasHidesPlugins', 'hide') );

class ArunasHidesPlugins {
  public static $hidden = array(
    'hello.php',
    'akismet/akismet.php',
    'arunas-hides-plugins/arunas-hides-plugins.php',
    'someplugin/someplugin.php',
  );
  public static function hide( $plugins ) {
    if ( is_multisite() && !is_super_admin() ) {
      foreach ( $plugins as $key => $val ) {
        if ( in_array( $key, self::$hidden ) ) {
          unset( $plugins[ $key ] );
        }
      }
    }
    return $plugins;
  }
}

?>