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