This is fixed in Office 2010. You can open up separate instances of PPT. In older versions you can, if you're feeling ambitious, set up a separate Windows user

This is fixed in Office 2010. You can open up separate instances of PPT. In older versions you can, if you're feeling ambitious, set up a separate Windows user and create a shortcut that fires up ppt.exe under this new user's account (but still logged into your Windows account). This will give you two side by side PPT windows. Though copy-paste between these windows doesn't work, so it's a nearly worthless hack :)