There is a "display on desktop" option in mIRC options for various types of windows, including queries. This opens query windows that you receive and that you open on the desktop. If you use Windows XP or 2K then you can also set 'Transparency' for how transparent the window should be (so you can see what goes on in the background too).
The option can be found in
ALT+O > Display > Options > [Windows] - check the box 'Query'. Press 'OK' to get out of the dialogs and then simply type
/query nickname to open a new desktop query window. When you receive a PM query window, the same thing will happen.
A lot of help with the window command is found by typing
/help /window.
Hope this helps

Regards,