Microsoft System Center 2012 SP1 adds a bunch of new features to the Suite of products. I have deployed it a few times at companies already without a lot of problems. The only issue I have encountered so far is with Software Updates "Remote configuration failed on WSUS Server" which is described HERE.
On MyITforum however there is a list created about System Center 2012 SP1 issues. This because there are a ton of reports coming in that SP1 is causing some frustrating issues in those companies that have decided to deploy it already. This Wiki post serves to capture the issues in a central location to ensure everyone is aware of them and their potential workarounds until Microsoft releases fixes.
As a member of myITforum and a member of this group you can modify this live document to include issues that you have encountered.
Source: System Center 2012 SP1 Woes, Gotchas, and Workarounds
The first hotfix is available already: ConfigMgr 2012 SP1 client hotfix for MicrosoftPolicyPlatformSetup.msi error available