You could use SNMP. There is an SNMP agent that comes with Windows and perl modules for SNMP that will certainly work on Linux

Alternatively, the Nagios project have several ways to monitor processes on Windows boxen. One way is with NSClient, which is an agent that is installed on Windows and queried from a Linux box using the check_nt plugin. You don't necessarily have to install the full Nagios product, just use the Nagios plugin from a perl script checking the exit status of the plugin.

There may also be some useful scripts on Nagios Exchange:

In reply to Re: To monitor windows processes using Perl by bingos
in thread To monitor windows processes using Perl by msk_0984

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