Ok, I know this thread is a bit old, but for the sake of others who stumble upon it, here's some more info.
Skype is certainly the #1 option, but internet speeds are often too slow to connect successfully. I have to make a scheduled conference call every week, so this wasn't reliable enough for me.
We used prepaid SIM cards all the way from Seattle to Bolivia and intend to do the same through the rest of the continent. The prices range, but never more than $10 and the more expensive ones usually come with free time.
Always ask the owner of the Kiosk to activate the SIM for you. Some countries (Mexico & El Salvador, and others) require an ID number to activate. Kiosk owners can generally call in and provide their ID number to get you going.
If you are calling internationally ask about promotions, packets or calling cards. All can save a ton of money and they are usually very easy to activate.
Because we are working and traveling we keep records of this crap on our website, if you want detailed phone/wifi by country check this page out: Central and South America Internet and Phone Reports | Life Remotely