Before starting implementing performance counters, be sure you are not using one of the following options:

– /3GB switch – is not supported http://support.microsoft.com/kb/933560

Reducing the size of the kernel mode memory buffers when in /3GB mode causes unacceptable

performance in Windows SharePoint Services file-transfer operations.

– Web gardens – http://support.microsoft.com/kb/822171/ IIS 6.0 Session State May Be Lost If You Use Web Gardens with ASP Applications

– Priority Boost on SQL server – http://support.microsoft.com/kb/319942 How to determine proper SQL Server configuration settings

By default, the priority boost setting is 0, which causes SQL Server to run at a normal priority whether you run SQL Server on a uniprocessor computer or on a symmetric multiprocessor (SMP) computer. If you set priority boost to 1, the SQL Server process runs at a high priority

Once you have removed all those options you can start implementing performance counters and start analyzing them.