If you want to change the system collation then you can rebuild the system databases from the install media.

You will want to script out all server objects like, jobs, logins, linked servers, DDL triggers etc.

Make sure you have backups of all your user databases and system databases as you will need to re-attach / restore them as the master database will know nothing about them as it will be like its a fresh server.

http://msdn.microsoft.com/en-gb/library/dd207003(v=sql.105).aspx