Which hotfixes should I apply?

Common OpsMgr 2007 Post-R2 hotfixes:

This list ABSOLUTELY assumes you are at OpsMgr R2-RTM level as a base (6.1.7221.0).

MP Update	Microsoft.SystemCenter.2007.mp 6.1.7695.0 Microsoft.SystemCenter.OperationsManager.2007.mp 6.1.7695.0 Microsoft.SystemCenter.OperationsManager.AM.DR.2007.mp 6.1.7695.0 Microsoft.SystemCenter.OperationsManager.Reports.2007.mp 6.1.7695.0 ODR.mp 6.1.7695.0	New reports, knowledge, monitors, rules. See MP Guide.	MP import only
2251525 R2 CU3	OpsMgr 2007 R2 CU3 Cumulative Update Multiple. See KB Article. Note this is a DLL update, MP updates, and SQL scripts update.	Many updates. See KB article for CU3, CU2, and CU1 for full list.	RMS MS GW Agents AuditCollector Console WebConsole MP Import TSQL Script
971233	none	The console shows customized subscriptions SMTP{GUID} after you upgrade to OpsMgr R2 from OpsMgr SP1	Operations Database (TSQL only)

Common OpsMgr 2007 Post-SP1 hotfixes:

This list ABSOLUTELY assumes you are at OpsMgr SP1 level as a base (6.0.6278.0). These DO NOT APPLY these to OpsMgr R2.

MP Update	Microsoft.SystemCenter.2007.mp 6.0.6709.0 Microsoft.SystemCenter. OperationsManager.2007.mp 6.0.6709.0 Microsoft.SystemCenter. OperationsManager.AM.DR.2007.mp 6.0.6709.0	Agent restarts, many other critical enhancements	Management Pack Import only (Import via console once extracted)
2028594	SP1 Cumulative Update 1. Multiple files. See KB article	Many. See KB article	RMS MS GW Agents Consoles MP Import SQL Scripts (OpsDB and DW)
971541	SP1 Rollup hotfix. Multiple files. See KB article	Many. See KB article	RMS MS GW Reporting Agents Console MP Import
972881	Managedentitychange.sp.sql	The changes to the display name of a managed entity are not synchronized in the Operations Manager Data Warehouse database	Data Warehouse Database (T-SQL only)
954643	Managementpackinstall.sp.sql	Event ID 31569 is logged after you install a management pack that includes reports on a System Center Operations Manager 2007 SP1 server	Data Warehouse Database (T-SQL only)
974254	Autotablecreation.sql Viewcreatesprocs.sql	1. Unable to create large number of groups. 2. Import fails when importing an MP or when creating a MP from a template	Operations Database (TSQL only)