Pop-Up Notification when time reaches 4:00PM?

As many of the other commenters said, the best way to do this on a daily basis is to use cron, but if you are only wanting to do it for one day, or sporadically, you can use the at command:

echo 'notify-send "Work day is done!"' | at 4:00PM 

You can use at in a variety of ways, including as a tea timer:

echo 'notify-send "Get your tea!"' | at now + 3 minutes 
echo 'notify-send "Meeting in 1 hour with the big boss!"' | at 1pm tomorrow 

It's quite useful for those one-off commands.

Check the at manpage for more syntax goodness.

Use notify-send to send the notification. Set it up as a cron job.

You can send commands to notify-osd like so:

notify-send "Go to bed!"

A crontab for daily notification at 4pm would look like so:

0 16 * * * /home/username/notify.sh