If you’re thinking about pulling the wp-content directory out of the main WordPress directory, don’t.

Moving the directory and replacing it with a symlink works, aside from one anoying bug: register_activation_hook (__FILE__,...) and register_deactivation_hook (__FILE__,...) will stop working due to a function called plugin_basename not knowing about the symlink.

That means that most of your plugins won’t be activated on activation nor deactivated on deactivation, and that may leed to strange and annoying bugs if the plugin touches WordPress’ rewrite_rules.