Main differences are listed below (in bold) that may swing the choice based on your company requirements.
Enterprise :
Complete EAI, B2B, and Business Process Management functionality
Includes all vertical industry accelerators (RosettaNet, HIPAA, HL7, and SWIFT)
Includes BizTalk Adapter Pack. Includes all current and new application and technology adapters
Includes BizTalk RFID Server and Mobile capabilities with support for unlimited devices
Supports High availability/Failover for multiple RFID Servers
Includes Host Integration Server
Unlimited "applications" allowed (see BizTalk Server 2009 Pricing and Licensing FAQ)
Scale out/failover multiple message boxes
Remote or local DB
Available for 120-day evaluation at no cost
Standard :
Complete EAI, B2B, and Business Process Management functionality
Includes all vertical industry accelerators (RosettaNet, HIPAA, HL7, and SWIFT)
Includes BizTalk Adapter Pack
Includes all current and new application and technology adapters
Includes BizTalk RFID Server and Mobile capabilities with support for unlimited devices
Includes Host Integration Server
Limited to two CPUs on a single server
Five "applications" allowed (see BizTalk Server 2009 Pricing and Licensing FAQ)
Single server solution/single message box
Remote or local DB
Limited 64-bit operating system support ***
*** Standard Edition supports 64-bit operating system but not in native 64-bit execution mode
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