J'ai jamais had problems running performance counters on mon servers.
Microsoft suggests watching following counters for IIS:
Memory\Pages/sec
Memory\Available Bytes
Memory\Committed Bytes
Memory\Pool Nonpaged Bytes
Processor\% Processor Time
Processor\Interrupts/sec
Processor\System Processor Queue Length
LogicalDisk\% Disk Time
PhysicalDisk\% Disk Time
LogicalDisk\Avg. Disk Queue Length
PhysicalDisk\Avg. Disk Queue Length
LogicalDisk\Avg. Disk Bytes/Transfer
PhysicalDisk\Avg. Disk Bytes/Transfer
System\Context Switches/sec
Web Service\Bytes Total/sec
Web Service\Total Method Requests/sec
Web Service\Current Connections
Web Service Cache\File Cache Hits %
Web Service Cache\Kernel:URI Cache Misses
Web Service Cache\Kernel:URI Cache Hits %
Specifically for ASP.NET I would watch
ASP.NET\Application Restarts
ASP.NET\Requests Queued
ASP.NET\Worker Process Restarts
ASP.NET Applications\Errors Total
ASP.NET Applications\Requests/Sec
ASP.NET Applications\Pipeline Instance Count
.NET CLR Exceptions# of Exceps Thrown
