When starting applications such as parcellite, dropbox which needs a system tray, their icons are missing from Gnome3 system tray. The issue is caused due to a bug in Gnome3 and is fixed in the latest update.
# yum update gnome*
Once the update is finished logout ( a reboot is recommended ) and login again.
Still you cannot see the icons in system tray??
Make sure you are checking at the right place. In Gnome3 the system tray is not at the top right hand corner. It is visible at the bottom right hand corner of the activities (alt + f1) screen.
See the screen shot below,
In fedora 20 you may have to click on the bottom edge of the Activities screen/window in order to reveal the system tray containing your icons.
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