I'd like to have this subject discussed much more often than it is nowadays. Military is on an extreme of the ethical-unethical scale but there are many more cases which would deeply fall into the unethical side of the scale and are not being talked about at all.
Sorry to complain about this but the current title - "Rob Conery will never run a .NET Open Source project again. Here's why." - reminds me of those sites abusing emotional linkbait titles. The "Here's why." part is telling. Can we please avoid this here?
WhatsApp is a closed-source proprietary app owned by Facebook. Metadata is owned and kept by them, and normal chat data is also theirs. They claim they have started using the textsecure encryption mechanisms on their apps, but this appears to only be true for the most-recent Andriod app. So there is a high probability some or all of your messages are either not encrypted or encrypted with a key that you do not have. For these messages the police or other government agency could retrieve via a warrant or other means. Whatsapp uses a subscription model and they can decide to change the terms or costs at any time, or discontinue the product. They are not very transparant and take a long time to implement changes / fixes that they promise will be implemented. The app has a very large user base in many markets.
Signal is a free open-source iOS app from whispersystems, licensed under the GPL. It's counterpart on Andriod is testsecure/redphone, which will eventually be reimplemented and rebranded as Signal for Andriod. It is secure by default, all messages are encrypted using private keys of the participants... whisper does not have they keys (so they can not turn the keys or content over to anyone). You can audit this since it is an open source app, and if you would like to fix a bug or work on a feature you can do that as well. It does not have nearly as big of a user base as WhatsApp, and needs some love before usability/features/bugginess are on-par which whatsapp (shouldn't be too hard to match as WhatsApp itself is not very feature rich and often quite buggy itself). Signal has taken it's time in development (Textsecure for iOS was 'on track' to be released in summer of 2013)...
You can also make secure phone calls with Signal/Redphone, but not WhatsApp.
Although it's not obvious, I guess popularity as a lot to do with ergonomics and usability and their evolution so something will only continue to be pushed forward if there's enough people to actually use it. I don't know, I'm just thinking out loud why something which has been on the market for such a long time only recently has seen such a crazy amount of innovation.