I am using 11.04 with Ubuntu Classic (no effects) session. I found that all the default applications have their indicator icons working fine. But for any other application ,which I installed like pidgin, fusion-icon, checkgmail etc, no icon appears in the notification area. These applications are indeed running as I could check from terminal. I checked with default Ubuntu session (which uses Unity) & found that icons are present and working as expected.
Also note that this is fresh installation of 11.04. I removed indicator-me and indicator-message. But icons (for new applications) do not appear even when they are installed. I want to use classic session as I am more comfortable with gnome 2.