Windows command line tool for disk IO monitoring

I am not sure about the exact type of data you are trying to collect, but all perfmon counter data is available via the typeperf command line utility even in Server 2003.

Sample use

List counters available (without instances):

typeperf -q

sample total CPU usage over 10 seconds once and return:

typeperf "Processor(_Total)\% Processor Time" -si 10 -sc 1

In general, all counters available through the perfmon GUI are also available through typeperf by the same name. Note that names may be localised on non-MUI systems.

The previous answer is good, but its example is for processor, not disk IO. Here is one for that:

typeperf -si 2 "\LogicalDisk(_Total)\Disk Bytes/sec"