Rebuild Master Database in SQL Server 2005 with Clustered Environment.

-. Start the SQL Server in Single User Mode 
You can skip the this step.

1. Run the SQL Server Configuration Manager

2. Changing SQL Server Startup Parameters
Add "-m;" in Startup Parameters

3. Restart the SQL Server Service.

- Rebuild the Master database.

start /wait <CD or DVD Drive>\setup.exe /qn VS=<VSName> INSTANCENAME=<InstanceName> REINSTALL=SQL_Engine REBUILDDATABASE=1 ADMINPASSWORD=<StrongPassword> SAPWD=<NewStrongPassword> SQLCOLLATION=<NewSystemCollation> SQLACCOUNT=<domain\user> SQLPASSWORD=<DomainUserPassword> AGTACCOUNT=<domain\user> AGTPASSWORD=<DomainUserPassword>

If you want to change collation, add SQLCOLLATION=<Collation>.
"ADMINPASSWORD=" means current logon account.

- Attach the user databases.

http://msdn.microsoft.com/en-us/library/ms143719(SQL.90).aspx