How to collect performance counters from several websites

I am investigating how to automaitcally collect .Net performance counters from web applications.
We have several web applications running on the same server and as result there seem to be no way to identify which performance counter instance to which application.

For instance in case of 2 web applications perf counter "# of current physical Threads" would have 2 instances:
1)  w3wp

2) wrwp#1

I know there is way to reformat instance name using registry key (ProcessNameFormat), but it would still be ambiguos name including ProcessId and we will not be able to identify which perf counter instance belong to wchih applciation.

Any suggestions on how to automatically track .Net counters with several application running?

Thank you

Andrey