And the article you linked points out several times that the encryption is only going to be enabled for WhatsApp's Android client for the time being.
We have XMPP and OTR, and with chatsecure on Android or various clients on Linux it's pretty pleasant. I believe there are a few OS X clients as well, not sure about iOS.
Threema is closed sourced and thus I don't know which/how encryption are they actually using.
Also, messages are not encrypted by default, and there is afaik no way to encrypt group chats. You have to create a special "secret" chat for the messages to be encrypted.
So far only TextSecure does this.
One needs to have source released, audited and verified to match prebuilt binaries that are actually used by the unwashed gray masses. Without all three checked for each public build you have zero assurance that you are running a binary built from the released source and that the source doesn't have anything fishy in it.
The only app that checks all three, somewhat ironically, is TrueCrypt. PGPfone checked #1 and #3. TextSecure checks just #1 unless I am missing something, so objectively its "demonstrated security" is exactly the same as that of any another app that simply describes what it does in plain English and has a traffic to prove it.
Telegram has fantastic clients on all the platforms, but isn't secure. TextSecure is secure, but has only a mediocre app on a single platform (Android). The other alternatives are even worse.
Tox is looking really promising though: https://wiki.tox.im/FAQ