I'm an advocate of personal privacy through encryption. I love the Threema instant messenger (Link) but none of my contacts used it. This is the problem with secure instant messenger apps, your friends aren't there so it becomes useless.
Now Whatsapp is including the encryption functionality of TextSecure from Open Whisper Systems in their Android client and this will make Whatsapp the most secure instant messenger (beating even Apple's a Messages/iMessage).
Like Whatsapp, Apple's iMessage/Messages offers end to end encryption but in Apple's design, they control the encryption keys which means they could create a man in the middle type situation and you would never know. In the new Whatsapp with encrypted messenger app, the keys are controlled by the client and you will be able to verify the counter-parties encryption key using QR code scanning (similar to Threema) or by verbally exchanging the encryption key verifier. This will make sure beyond any doubt that the messages are encrypted for the intended recipient and no one else.
How will it work?
When you start a conversation with another Whatsapp android users using the latest version, you will be asked to initiate a secure session. Once initiated, you will see visual marker (lock icon) in a couple of places to remind you the session is protected : next to the send button, next to each encrypted message and in the title bar.
If you are using the latest android client, your version already includes the new end-to-end encryption mechanism and it is activated when talking to other Android based Whatsapp users.
Although I haven't seen any promises for an IOS version upgrade containing this secure technology from Whatsapp, I am confident we will eventually see it on iPhone as well.