Pidgin is a chat program that is available for all popular operating systems, and that speaks virtually all chat and messenger protocols (Yahoo, ICQ, MSN, Skype, Jabber, IRC...). Just insert into "Preferences" under "Network" the connection data for JonDo (Host=127.0.0.1, Port=4001), and immediately all chat data go over JonDo. Moreover, you should create all of your chat accounts anonymously using JonDo and use OTR for encrypting your communication.

Hint: If you are using several chat accounts, the chat server may observe concurrent logins. Thereby, it may match these accounts to the same person. You should therefore either use several chat servers or always activate only one account at a time in Pidgin.