Actually you very well can play PQ on your windows machine. You can use the emulator included with Microsoft eMbedded Visual Tools (available from pocketpc.com developer section, the pack is several hundred MB large). Then you can compile PQ using the PQ source code and eVC++, which is also in the eMbedded toolkit.
As an alternative you can find a precompiled emulator PQ here:
http://mzguy.zapto.org/files/PocketQuake.exe
Use that with the emulator and you can play PQ in windows with insane FPS speeds
[edit] I believe you need an NT based OS, like Windows NT, 2k or XP (or .NET) to use the emulator.