Middle holds the code I'm working on (Notepad2, Delphi, midnight commander or most likely vim - with PuTTY maximised.)
Windows taskbar sits at the top of the middle screen, as it feels most natural to me... (given I have no choice of OS at work).
Finally on the right, php.net or Delphi's awesome help files, or even some reference material from stackoverflow (WIN). Slashdot sits in a tab at the back there.
Most importantly, with 3 screens I've never felt I don't have enough space. My brain can only handle 2 things at once (i.e. code and code output, or stackoverflow and code, or code output and the email I'm copying it into, etc) ... but my brain (personally) gets distracted if I loose something "behind" another. So having that 3rd screen lets me have 3 things open, switching between any combination of a pair.
I like having them big enough for my poor eye sight, reasonably low brightness setting (with high contrast). Different white balance annoys me, but that's a personal thing purely.
Finally, they have to be high enough. I'm tall, and I sit upon a gym ball to try and enforce my naturally awful posture. Having the screens a little higher than recommended relieves my neck pain hugely. (Someone will no doubt tell me I'm wrong here! I personally find it works well, judging by how well I sleep at late.)
A non-distracting wallpaper (solid colour) or a good MacOSX shipped offering and no icons (no, not one!) ... they distract me hugely. And a little tip from myself, have the two on the left/right slightly lower (if your taskbar is at the top, or slightly higher if the bottom) so you can move straight to the start button and system tray and have Windows "corner" your mouse cursor for you (without it flying off to another screen).
I've met several good programmers who swear 2 is enough, I've secretly sourced and subtly (like a ninja) installed a 3rd screen for them, they didn't even notice for the first few hours. They've all eventually converted.
It's not about *using* all three, it's about having the room to spread work out, without having to context switch yourself between stacks of windows. Well, at least it is for me.