My first choice would always be Web Services (preferably WCF although you need BTS 2006 R2)
Legacy protocols like File and FTP should only be used when you have no other choice. These protocols require other software components to deliver messages and there is no continuity between sender and receiver.
HTTP is similar to Web Service, although is a lower level protocol – no metadata discovery, less options for security (restricted to HTTPS/SSL for authentication and encryption)
Queuing is an definite option for asynchronous messages when you cannot rely on the end-points being available, and you do not wish to handle error recovery/retries in your client code. WCF reliable messaging is not yet at the stage to replace MSMQ or Websphere MQ ( no underlying message persistence)
Using WCF will enable you to use a similar interface model for Biztalk delivered services and other services using the WS-* protocols.