The link below is an extremely useful article when is comes to troubleshooting your Unix / Linux discoveries with SCOM 2012.
Something I came across which I did not see in this article, you might get the following error during your discovery:
Unexpected DiscoveryResult.ErrorData type. Please file bug report. ErrorData: Microsoft.SystemCenter.CrossPlatform.ClientLibrary.MPAbstractions.InvalidWSManTaskResponseException Failed to parse output from WSMan discovery. Output from task was: <DataItem type=”Microsoft.SystemCenter.WSManagement.WSManData” time=”2013-02-26T15:35:00.1849706+02:00″ sourceHealthServiceId=”16F56055-5671-604C-AF9D-088444BA4B6E”><WsManData><ErrorCode>0x800703fa</ErrorCode><ErrorMessage>Illegal operation attempted on a registry key that has been marked for deletion. </ErrorMessage></WsManData></DataItem>. at System.Activities.WorkflowApplication.Invoke(Activity activity, IDictionary`2 inputs, WorkflowInstanceExtensionManager extensions, TimeSpan timeout) at System.Activities.WorkflowInvoker.Invoke(Activity workflow, IDictionary`2 inputs, TimeSpan timeout, WorkflowInstanceExtensionManager extensions) at Microsoft.SystemCenter.CrossPlatform.ClientActions.DefaultDiscovery.InvokeWorkflow(IManagedObject managementActionPoint, DiscoveryTargetEndpoint criteria, IInstallableAgents installableAgents)
If this happens all you need to do is restart your SCOM services on the management server that is running your discovery, it will then complete.