A sentence for a person who is greatly tired
In addition to izx's comment, keep up the good work is often used as a phrase of encouragement and to keep people motivated.
You could also substitute any of the following for good -- great, fantastic, exceptional, &c depending upon how impressed you are with their work or how much encouragement you want to give to them.
You could say, "Hang in there", which is an informal exhortation, basically meant to encourage someone: "keep on doing what you're doing, and don't be discouraged, even in the face of adversity, hardship, opposition, or fatigue".
This is often done in a somewhat joking manner, e.g.
"Good job, don't work too hard!" with a smile and a chuckle.
Also:
"Nice work, make sure you take a break!"
or
"Wow, that's great, it must have taken forever" (can imply mucho time spend already - sometimes).