Sriram,
In response to your questions:
– To implement synchronous communications with BizTalk, you might want to consider using something other than MSMQ because MSMQ does not inherently support synchronous communication. WCF handles sync communications much more naturally than MSMQ. In BizTalk, one of the best ways to implement request/response communications is to publish a request/response WCF service. You can do this with MSMQ, but you would have to write some custom app to front MSMQ, such as a web or WCF service.
– Yes, you could write a C# Windows service to poll the queue on the BizTalk server. The benefit to this would be that you get durable communication (the apps can send messages to each other without caring if the other one is up). Well guess what, when BizTalk sends messages, it doesn’t really need MSMQ for durable communication. BizTalk itself is a message queue, so you could expose a WCF service from your app for BizTalk to submit messages into. If your app is down, then BizTalk can retry submitting the message until your app comes back up.
Hope this helps!