as of version 2.5, we have the auto-upgrade/new version notifier for plugins. While i love the fact that i get notified that there is a new version of a certain plugin, i cannot see for which plugins i'm not going to get this notification.
for example "role manager" is not hosted on wordpress.org, so i won't get a notification if it's updated. Maybe there can be an icon, different color or another kind of marking or maybe even a split list of plugins so i know which plugins i have to check manually and which i don't have to pay attention to.