Index Errors or The store ‘avm://sitestore’ has a duplicate root node entry:

Whoops, you’ve inadvertently done something Very Bad to your Alfresco install and the application throws a fit about the indexes when you try to start it up.  There’s a problem with the database data and the lucene indexes being out of synch.

To solve this error you need to rebuild the lucene indexes.  To do this:
1.  Stop Alfresco.
2.  Delete everything under /alf_data/lucene-indexes
3.  Edit C:/Alfresco/tomcat/shared/classes/alfresco/extension/custom-repository.properties or
alfresco.war/WEB-INF/classes/alfresco/extension/customer-repository.properties to set the property index mode to AUTO instead of validate
4. Start Alfresco again.

customer-repository.properties:
index.recovery.mode=AUTO
Now instead of validating the indexes and failing, the indexes will be rebuilt if a problem is found.

java.lang.UnsatisfiedLinkError: no Win32NetBIOS in java.library.path:

You need to add the folder containing the Win32NetBIOS.dll and Win32Utils.dll to the java.library.path of your application server.  For JBoss make an entry in run.bat
set JAVA_OPTS=%JAVA_OPTS%  -Djava.library.path="C:Alfrescobin"

The server should now be able to find the files.