I am so, so sorry for the loss of your partner.
Check out The Invisible String - a beautifully written book that may be of help to her and can give something tangible that she can understand and discuss with you - and may help her feel closer to her father when she is feeling down.
http://www.amazon.com/The-Invisible-String-Patrice-Karst/dp/0875167349
Some of these books listed talk about the way families come in all different shapes and sizes.
This list contains books that feature single parent households.
The Invisible String features a family with two siblings and a mum that talks about how we are all connected and love each other despite distance or absence. The book could help the children feel represented and it's an important message. Conversation the mum has during reading could focus the message on the children being loved by their father even though he isn't around (regardless of his true feelings). Even if that isn't the message she wants to share, it touches on everything from being away at school, death, friends, etc.
I don't have any great advice or wisdom, but I would definitely suggest getting creative with ways to stay in touch. Send him mail, postcards, drawings that you start and he finishes, stories about a made-up place you invent together, even a small toy or cut-out you can send back and forth to take photos with (a la Flat Stanley). You can watch movies together (think Netlfix lets you do this?), maybe even find a simple multiplayer game online. Make sure he has a good printed picture of you two together, and show him that you have a copy of it too (framed, or in your wallet, or wherever). You might check out the book The Invisible String for a cool way to imagine being connected even when you're far away from each other. Night Catch is another good one, written for military families but could definitely apply here too. Best of luck - your son is lucky to have a Dad who cares so much!
http://www.amazon.com/The-Invisible-String-Patrice-Karst/dp/0875167349
This book might be worth trying