Breaking changes between 2008R2 RTM going to 2008R2 SP3?
Consider this as answer

SP3 is new and thoroughly tested its highly unlikely it would create any issue but again I would recommend you not to proceed without any testing and that too when Cluster is involved. Also asking whether anybody faced issue will lead you in problem, what if somebody writes 'Yes I have done and its working fine' yes they are correct it worked in there environment but I am sure your and his environment are not same and after applying SP if something stops working who would you catch other than Microsoft.

I have applied SP3 in my environment and every thing is going good as of now. But if you ask my plan of action I have now deployed in DEV then I will deploy in UAT and then after a month, because couple of SSIS packages run monthly, I would apply in production.

Please create an environment and test first believe me it will save you lot of hassle.

If still you want to proceed

1.. Backup system and user databases. Use TSQL backup command [This link is external to TechNet Wiki. It will open in a new window.] or SQL Server Management studio GUI [This link is external to TechNet Wiki. It will open in a new window.] to backup system and user databases. Since you backup system and user databases you don't need to backup jobs, SSIS packages, mail profiles, linked servers  and logins as all of these would be included in MSDB and Master database backups.


If you use analysis services backup Analysis Service configuration files, databases and repositories. Backup files present at location
C:\Program Files\Microsoft SQL Server\MSAS11.\OLAP\Data\
C:\Program Files\Microsoft SQL Server\MSAS11.\OLAP\Config\ directory.
Make sure enough space is available on drive where resource/system databases are present. Resource database [This link is external to TechNet Wiki. It will open in a new window.] is utilized during service pack upgrade. The Resource database makes upgrading to a new version of SQL Server an easier and faster procedure. In earlier versions of SQL Server, upgrading required dropping and creating system objects. Because the Resource database file contains all system objects, an upgrade is now accomplished simply by copying the single Resource database file to the local server.
Service pack upgrade would require a downtime of application. Make sure application does not access database during service pack upgrade. Make sure you stop all jobs and activities on database before proceeding. you don't need to shutdown database services to apply service pack.
Make sure you are administrator on the system and always run the service pack executable with administrator privileges.


Please do read This BOL