I have a dualmonitor setup using 2 screens in my xorg.conf file - :0.0 and :0.1 As a result I can move my cursor between screens easily, but I cannot drag application windows across the screen border.

I have played with making one big screen stretch across both monitors, but for a few odd reasons I like this setup better. It would, however, be very nice if I could send application windows back and forth from screen to screen.

Given a window's ID (xwininfo), is there a command that I can enter from a prompt that will send that window to the screen of my choosing?

(I am using Fluxbox so I assume that there is nothing prebuilt that will do this unless I script it up myself)

you would want to enable Xinerama in the ServerLayout section of your xorg.conf

No, not exactly - the way that it works without Xinerama is the way that I want to keep it. I just want to be able to send windows back and forth in a not-necessarily-user-friendly manner. Generally I will spawn the application on the screen that I want it to remain - I just need some way to change my mind as needed.

X was built to server a massive multiuser system - I can't believe that there isn't a way, say, for root to take a Windows owned by one screen and stick it on another.

You could try a tool designed for your graphics card. I am pretty sure ATI's official drivers allow you to set up 2 screens as 2 different desktops in KDE. This way you can right click on the header and send to Desktop2 to send it to the 2nd monitor.