Notify-send is a great application for notifying you when an event has occurred. An event such as a script running to completion.

If notify-send is not installed on your machine already, install the package "libnotify1" (or possibly just "libnotify") from your repositories.

Once installed you can simply type the following, at the command line, to display a pop-up message near your system tray:

notify-send "hello"

By default the message will be displayed for 5 seconds. To change how long a message stays displayed use the "-t" switch. This will change, in milliseconds, how long the message is displayed. Enter "-t 0" to leave the message up until the user closes it.

notify-send "This message will be displayed for 3 seconds" -t 3000
notify-send "Click me to close me." -t 0

You can even add a title and an icon to the notification.

notify-send "This is the Title" \
            "Check out the cool icon" \
            -i /usr/share/pixmaps/gnome-terminal.png

When used in a script you could set it to notify you periodically by placing the command in a loop:

#!/bin/bash

while [ 1 ]; do
     notify-send "Up Time" "`uptime`"
     sleep 5m
done