I saw a demo last week about BizTalk + Host Integration Server (HIS). I believe that HIS 2006 falls underneath the same license as BizTalk Server 2006/2006R2. I would start there (HIS 2006). In the demo they did integrate some .Net code with COBOL running on a IBM Mainframe. They then showed how you could do it using BizTalk.
This is about all I know about it. I certainly know that you can do it. I cannot speak to how well it works, how easy/hard it is etc.