Among all the messaging apps out there, WhatsApp was targeted the most. It was blocked either fully or partially in 12 out of the 65 countries Freedom House looked into. In Brazil, for instance, the government blocked the service a few times for refusing to hand over encrypted chat data related to a drug investigation. It was also blocked in Uganda during the presidential elections in February and during the reelected president's inauguration in May reportedly to suppress people's discontent over the results.
You can read Freedom House's full report on the organization's website, including a ranking of countries with the most internet freedom to the least. Estonia apparently enjoys the most freedom, while China with its infamous "Great Firewall" has the most restricted internet in the world.