How do I clear all gnome shell notifications?

Shamelessly using this workaround from the Fedora forums here.

You can reset the gnome-shell by typing Alt+F2, entering r and hitting enter. This resets/restarts the GNOME Shell and so clears all notifications.

If this is still bothering you, I've found a workaround for using jupiter. The trick is to add the transient hint to the notifications that jupter sends.

For me (installed jupiter via webupd8 ppa on 11.10), the appropriate file to modify is /usr/lib/jupiter/scripts/notify

For my setup, the change I had to make was to add --hint int:transient:1 to every call of notify-send within the script. Thus, my jupiter notify script changed from:

    function notify {
      if [ ! "$NO_NOTIFY" = "1" ]; then
        ICON=$2
        MESSAGE=$1
        if [ "$DISTRIB_RELEASE" = "9.10" ]; then
          DISPLAY=:0.0 /usr/bin/notify-send -i $ICON -t 1500 "$MESSAGE" 2>/dev/null
        else
          USER=$(who | sed -n '/ (:0[\.0]*)$\| :0 /{s/ .*//p;q}')
          USERCNT=$(who | wc -l)
          if [ ! "$(whoami)" = "$USER" ]; then
            if [ ! "$USERCNT" -lt 1 ]; then
               su $USER -l -c "DISPLAY=:0.0 /usr/bin/notify-send -i $ICON -t 700 \"$MESSAGE\" 2>/dev/null"
            fi
        else
            if [ ! "$USERCNT" -lt 1 ]; then
             /usr/bin/notify-send -i $ICON -t 700 "$MESSAGE" 2>/dev/null
            fi
          fi
        fi
      fi
    }

to:

    function notify {
      if [ ! "$NO_NOTIFY" = "1" ]; then
        ICON=$2
        MESSAGE=$1
        if [ "$DISTRIB_RELEASE" = "9.10" ]; then
          DISPLAY=:0.0 /usr/bin/notify-send --hint int:transient:1 -i $ICON -t 1500 "$MESSAGE" 2>/dev/null
        else
          USER=$(who | sed -n '/ (:0[\.0]*)$\| :0 /{s/ .*//p;q}')
          USERCNT=$(who | wc -l)
          if [ ! "$(whoami)" = "$USER" ]; then
            if [ ! "$USERCNT" -lt 1 ]; then
               su $USER -l -c "DISPLAY=:0.0 /usr/bin/notify-send --hint int:transient:1 -i $ICON -t 700 \"$MESSAGE\" 2>/dev/null"
            fi
        else
            if [ ! "$USERCNT" -lt 1 ]; then
             /usr/bin/notify-send --hint int:transient:1 -i $ICON -t 700 "$MESSAGE" 2>/dev/null
            fi
          fi
        fi
      fi
    }

This isn't really a direct answer to your question, since this won't clear all notifications, but it will at least prevent the jupiter ones from stacking up.

Hope this helps!