<p>I have a pretty much default installation on mysql on Windows 2003. I am rebuilding some indexes and the process only seems to use 3-20% of the CPU.</p>

<p>Is there a way to allow it to use more and speed up the process?</p>

This applies to every application/process, not only mysql. If your database is using 3-20% CPU and the final performance is still unacceptable it means that you don't lack processor power, since it is most of the time idle. What is most probable is your bottleneck is at your HDD or HDD-controller level. Have you tested the I/O bandwitch and access time of your HD?