1. Download "dxwnd" from http://sourceforge.net/projects/dxwnd/ unpack it and start dxwnd.exe

2. Right-click on the white space in dxwnd and select "Add". Make sure "path" links to the POP3.exe! After filling out the empty spaces it should look like this: (My path for example is 'C:\Program Files (x86)\Steam\SteamApps\common\Prince of Persia Two Thrones\POP3.EXE')

You now should be able to play T2T windowed by simply starting it normally (= starting it the normal way / given that dxwnd is opened of course).

Edit: I'm on Windows 7 with the steam version. If you're not on Win7 I can't guarantee that this will work for you. (It should though in most cases)