Here are some Microsoft Exchange counters that you should monitor on the Performance Logs and Alerts program.

Memory

-Avaiable MBytes
* Value should be greater than 10MB

-Pages/sec
* Value should be less than 50 pages per second

-Pool NonPaged Bytes
* Value should be under 100MB

Disk

-Avg Queue Length (Total)
* Value should be less than 2 requests

-Avg Disk Read Queue Length
* Value should be less than 2 requests

-Avg Disk Write Queue Length
* Value should be less than 2 requests

-% Disk Time
* Value should be under 60%

-Avg Disk Bytes/Transfer
* Value should be above 15KB

-Avg Disk Sec/ Read
* Value should be less than 0.05/sec

Processor
*If multiple CPUs then times the value by the numbers of CPU

-% Processor Time (Total)
* Value shouldn’t be more than 80% for 5 minutes

Process

-% Processor Time (Store)
*Value shouldn’t be more than 75% for 5 minutes

-% Processor Time(System)
*Value shouldn’t be more than 75% for 5 minutes

-% Processor Time(Inetinfo)
*Value shouldn’t be more than 75% for 5 minutes

Use these to help you to determine if you Exchange Server is bottleneck or not.