I want to use PerfMon to measure memory usage of the application over time, however, there are more than dozen Memory related counters.
Which one will give me an accurate picture?
Process/Private Bytes will give you the memory for the worker process. Process/Virtual Bytes or Process/Working Set will give you virtual memory. You can do some easy searches to learn how to analyze the data you get after monitoring and see either or both of those counters rising.