I use the following command when I stuff up the collation:

start /wait setup.exe /qb INSTANCENAME=MSSQLSERVER REINSTALL=SQL_Engine REBUILDDATABASE=1 SAPWD=Password01 SQLCOLLATION=SQL_Latin1_General_CP1_CI_AS

There are various other switches etc - refer BOL. Yes it does rebuild the master database, this is for when you realise early enough that you have stuffed up. Which I obviously have done enough times to make it worthwhile hanging on to this command 🙂

pcd