If you've been on the phone for awhile and this happens, I'd say maybe the conversation has died a natural death so just end the call and in the future, keep the calls shorter.
If your friend is like this from the start, then she's not the type to stay focused and if she's been like this for years, she's probably not going to change. So accept it and maybe only talk to her in person. Or, IM her on FB and have an online conversation if she's more inclined to participate if she has to focus harder because she's typing.
If you want to say something, then say something. But I'd try to say something meaningful like "When I was talking to you about how sad I was over the Newtown shooting, and how my job search is so hard at this time of year, I was very hurt that you seemed distracted by the computer and weren't fully "into" the conversation." instead of just pointing out she's not participating. I'm curious though, if she's distracted listening to you, does she talk at all herself? Or is the conversation more one sided on your part? Maybe she's just not a phone person.