Paul,
As the product of an "every other weekend dad," I want to encourage you to establish traditions and rituals that you and your son do together that you know his other parent doesn't do. For example, my dad started reading novels to us. He read the whole Chronicles of Narnia series and Lord of the Rings trilogy when we were little. He took us to art shows and music festivals. He took us on hikes where we got to pick out what we wanted in our lunches the night before. He got us hiking boots and walking sticks that we kept at his house. He also made a big deal of Halloween: made elaborate costumes, carved pumpkins and took us out Trick or Treating. All of these were things my mom either wasn't into, didn't have time for, or couldn't afford. It exposed us to new things and gave us something to look forward to that were just "dad things."
The other suggestions I would have require support from the other parent, so I'm not sure how useful they will be.
1. Get on Skype and call him every day or every other day so you can "see" each other. Maybe you can eat breakfast "together" or you can read him a bedtime story and be able to show him the pictures.
2. Make DVDs of you two reading bedtime stories that he can play before he goes to bed, or whenever he wants.
3. Send mail. A couple times a week, send him a card, postcard, a page from a coloring book, a picture of the two of you, a coupon for an ice cream cone, stickers, etc. I realize he's not reading yet, but it is a thrill for a little one to receive mail with HIS name on the envelope!
Just letting him know that you are thinking of him when he is not with you goes a long way. It sounds like you are doing the best you can given the circumstances.
Cheers,
A.