We've been working on a transition plan for a while now. The desktop team put together a list of applications that are affected by the transition and people have started to post design recommendations, filing bugs, and fixing applications. Any help talking to application developers of your favorite applications is always welcome!
KDE applications all work (application indicators are based on the same KSNI technology) and everything we ship on the CD is ported. Many applications are also just porting to the technology on their own. Application Indicators specifically have a fallback mechanism in place so that application authors can use them without having to break on systems that use the old notification area.
In Unity when I use an application that doesn't use application indicators remember that the icon for the application is sitting in the launcher too, so it's not like it totally disappears from your view, it's just not sitting in the top right of the panel.
For 11.04 there is a whitelist for applications that need to use the area. Users can modify this list to add legacy apps if they require it.
(Omar has information on what will happen to other apps.)