As the parent of a toddler who lost his father at a young age, I've spent much of my time as a parent dealing with this very question. Because he was only 8 months old when his father passed, he doesn't have much memory of his Daddy so our situation isn't quite the same as those whose children were older when they lost their parent, or children whose parent is away. But we face the pain of that absence in much the same way. He is almost 3 years old now and the absence of his father is really beginning to affect him.
The most important thing I have done to comfort our son is to make his father present in his life. We talk about Daddy all the time. I make comments about him throughout our daily routine, like showing our son Daddy's favorite candy when he is picking some out at the store or telling him that was Daddy's favorite color crayon too. We look at pictures, especially ones of the two of them together, and I tell him stories. I am fortunate to have videos of my husband reading storybooks (I asked him to do that before he left on deployment), so we watch those together some evenings and it really helps him to see Daddy and hear his voice. I had a "Daddy doll" pillow made before his father left on deployment, and our son has slept with it every night since, so we say our prayers at night with him there with us and kiss him goodnight before bed. I've also started certain traditions with him, such as letting balloons with messages go "up to Daddy" on special occasions and when we are outside we always look for our "Daddy cloud" and wave hello.
A lot of these same things can be applied to a child who is missing a parent who is away for work or on deployment, just tailor them to fit your specific situation. For us, the most important thing has simply been to keep him present. If you find ways to work his spirit into your daily life, he will always be there with your child. ♥