Surely they didn't use plaintext?!
I can't speak for written messages but the Allies developed a clever way way of encrypting voice communications using a system called SIGSALY. The Axis powers were never able to crack the encryption.
Basically, the way it worked was that random electronic tones and buzzes were pressed onto vinyl records and the records were stored at each end of the lines of communication. A person could then speak their message into a microphone on one end while a record was being played. On the receiving end, the same record had to be played perfectly simultaneously as the other record in order for the voice to be heard clearly.
It's obviously much more complicated than that as the equipment involved took up massive amounts of space and the technology serves as the foundation for all the crypto and digital communication we use today.
For more information, there's a chapter in delightful book on the history of the vocoder and synthesized speech called How to Wreck a Nice Beach by Dave Tompkins.
There was an interesting case of the failure of US cryptography in the dispatches of Col. Bonner Fellers, a military attaché in Egypt who transmitted extensive details on Brittish troop movements back to Washington starting in 1940. Since he was transmitting from the embassy he was restricted to using the "Black Code" which had been stolen by the Italians.
The leaks included many details of the African and Mediterranian operations. Cryptographic results were often in Rommel's hands within 8 hours, and Feller's pessimism about the Brittish situation played into Rommel's decision to drive towards Alexandria.
The code was changed in June 1942.
Sources at http://ww2today.com/new/2014-2/how-i-discovered-world-war-iis-greatest-spy
The US military made famous use of Navajo code talkers.
Not an encryption technique, but the British Army has a history of using Welsh speakers for communications that don't need to be strictly encrypted but are still a bit sensitive. This was used quite recently in the Balkan wars. I can't find any verifiable source that they were used this way in WW2, outside of specific Welsh Regiments using Welsh, but it would have been a bit of an oversight if the leadership didn't at least consider it.
http://www.independent.co.uk/news/welsh-speak-up-for-their-ancient-tongue-1311562.html
A whole wealth of info for all countries, from devices to history and coding breakthrough and transcriptions can be found here: