You have a few options, but part of it depends upon your version of SAP as well. If you are running ECC 6.0 then it is possible to start using some of SAP’s provided web services over SOAP 1.1 Basic profile. From what I have been told by SAP, if you need to get into reliable messaging (or the WSE stack) then you should look into connecting to SAP via SAP XI(PI).
Other options include the SAP adapter(s). With BizTalk 2006 R1 you have an adapter based upon the .Net Connector where as with BizTalk Server 2006 R2 (and above) you can use the WCF based SAP LOB Adapter. Within these adapters you can call BAPIs, RFCs or IDocs.
At my shop we integrate primarily using IDocs, but every organization is different.