Simple plugin that prevents requests for updats for a given list of plugins.

lock-plugins.php

<?php
/*
 * Plugin Name:     Lock plugin updates
 * Description:     Prevent plugin updates
 * Version:         1.0.0
 * Author:          daggerhart
 */

add_filter( 'http_request_args', 'lock_plugins_http_request_args', 5, 2 );

/**
 * Prevent lookup of certain plugin updates
 * Source: https://markjaquith.wordpress.com/2009/12/14/excluding-your-plugin-or-theme-from-update-checks/
 *
 * @param $request
 * @param $url
 *
 * @return mixed
 */
function lock_plugins_http_request_args( $request, $url ) {
  if ( FALSE === strpos( $url, '//api.wordpress.org/plugins/update-check' ) ) {
    return $request; // Not a plugin update request. Bail immediately.
  }

  if ( empty($request['body']['plugins']) ){
    return $request;
  }

  $plugins = json_decode( $request['body']['plugins'], true );

  // get a list of locked plugins from somewhere
  $locked_plugins = apply_filters('lock_plugins-locked_plugins', array());

  foreach( $locked_plugins as $locked_plugin_basename )
  {
    $active_index = array_search( $locked_plugin_basename, $plugins->active );
    unset( $plugins->active[ $active_index ] );
    unset( $plugins->plugins[ $locked_plugin_basename ] );
  }

  $request['body']['plugins'] = wp_json_encode( $plugins );
  return $request;
}

Inspiration: https://twitter.com/danielbachhuber/status/768907891294121984

Usage:

add_filter('lock_plugins-locked_plugins', function($plugins){
  $plugins[] = 'akismet/akismet.php';
});

Nice plugin. But I get some nasty PHP Warnings. You try to get properties of non-object.

I fixed 2 things:

1. First in line 34-39:

foreach( $locked_plugins as $locked_plugin_basename )
  {
    $active_index = array_search( $locked_plugin_basename, $plugins['active'] );
    unset( $plugins['active'][ $active_index ] );
    unset( $plugins['plugins'][ $locked_plugin_basename ] );
  }

2. In your comment you call the filter but do not return the array:

add_filter('lock_plugins-locked_plugins', function($plugins){
  $plugins[] = 'akismet/akismet.php';

  return $plugins;
});

Awesome, thanks for the help @obstschale. In case something else comes up, I went ahead and made this into a real repo--
https://github.com/daggerhart/lock-plugins