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A default installation of BizTalk Server 2002 hosed up my IIS metabase.  Attempting to reconstruct is was harder than I thought, since I could find no documentation on what virtual directories were setup and with which permissions.  I hope to save you the same pain.  Here is what I found out:

BiztalkServerRepository
Link to:  C:\Program Files\Microsoft BizTalk Server\BizTalkServerRepository
All permissions except script source access

BizTalkServerDocs
Link to:  C:\Program Files\Microsoft BizTalk Server\Documentation
All permissions except script source access

BizTalkTracking
Link to:  C:\Program Files\Microsoft BizTalk Server\BizTalkTracking
All permissions except script source access
Disable anonymous access

MessagingManager
Link to:  C:\Program Files\Microsoft BizTalk Server\MessagingManager
All permissions except script source access
Disable anonymous access