My colleague Matt has directed me to a quality paper explaining the difference between all of Microsoft's integration technologies and where each is appropriate. It covers Indigo, MSMQ, SQL Server Broker, SQL Server Replication, SQL Server Integration Services, BizTalk and Host Integration Server.
You can get it from here although you'll have to be part of a BizTalk mailing list in order to get access to it.
Thoroughly recommended!
-Jamie