It having been almost two months since I asked this question, and with the knowledge and observation of what I’m doing with two monitors over that time, here’s an update and what I’m currently thinking. I’d be happy to have additional answers to consider!

Two widescreen monitors is too much real estate to take in as primary workspace. (2 @ 1920x1200) My peripheral vision is pretty good, and when I’m sitting at a reasonable ergonomic distance from the center seam of the two screens, the outside edges are just not visible. Even refocusing eyes doesn’t work, it’s too far off to the edge of my eyeglasses, I have to turn my head to see the edge of a screen. So, that leads to my first principle in deciding what goes on which screen:

First Principle: One Screen is Primary, and centered in front of me

The Primary screen has the task I am currently focusing on front and center. (Thanks @Firejava for your description of this in your answer) Whatever program I’m working in Right Now is what’s there, either full or half screen. Windows 7 and the wide screen makes it quite practical to have two applications open and in the foreground. (Win+{leftarrow}, Win+{rightarrow} to place the app windows). Typical for me is Word and Firefox (2 apps each half screen) or Eclipse (full screen).

Second Principle: Secondary Screen(s) hold reference material. Usually.

Most of the time, my secondary screen has things that I want easily available, but not my primary focus. I usually turn my head to see them, rather than move windows between screens. I keep my Jira dashboard there, and often my Outlook Tasks list, each half screen. Other windows may land in front of those, often the Eclipse console view, or tabs I pull out of my Primary screen Firefox to keep visible. When I’m doing something that requires real-time monitoring of multiple systems, for example performance monitoring of a multiple tier web service test, spreading the profiler windows across the secondary screen so I can see 3 or 4 systems at the same time is very helpful.

As @qdev76 noted in his answer, the primary productivity benefit of multiple monitors is reducing the overhead of switching windows to bring something to the foreground. Both the physical overhead of key or mouse to bring windows to the foreground, and the cognitive overhead of finding the window you want. Having more space available to have multiple windows in the foreground is the value of multiple monitors. With a risk, which leads to my third principle.

Third Principle: Close, Minimize, or Force Distractions to the Background

All that visible screen runs a high risk of having windows open and visible that are a distraction and detriment to productivity. There’s a fine balance between having windows up and available so I can get to them quickly and easily when needed, and having windows open that distract my attention and pull my focus away from whatever task I should be working on right now. The overhead of starting most processes on my workstation isn’t very large, so I aggressively close things when I’m done with them. There are a few that do take a noticeable amount of time to start, and I try hard to minimize them when I’m not using them but expect to go back later today. Eclipse is a good example.

Outlook is a special case I haven’t sorted out to my satisfaction yet. I use Outlook Tasks, which I keep open in their own window, currently on my secondary screen. I can get to it quickly when I want to check the task list or add something to it, but it isn’t in my main field of focus all the time. I’m still experimenting with the primary Outlook window. I have used a custom dashboard as my “Outlook Today” view for years, with calendar, inbox, folders, and tasks all visible in one view. With Tasks on the second monitor, the dashboard becomes less useful and potentially more of a distraction. But I’m so used to having it up and the calendar available at a glance, it feels very odd to minimize it. Still a work in progress.

Overall, I think having a second monitor is a nice convenience and I’m liking it, but I haven’t yet seen the boost in productivity other people claim. I did get that kind of boost when I went from a 4:3 monitor to a wide screen, so maybe I’ve already learned how to use “extra” space well enough that gains here will be incremental rather than exponential.

I used to have a 24" LCD in addition with my MBP 15". Here are some of the use cases:

• Coding: IDE on primary screen and resource on secondary screen.
• Reading: Take notes on primary, material on secondary.
• Web programming: IDE on primary, webpage result on secondary.
• productivity: GTD tools on secondary for reference, e.g. OmniFocus or Evernote where you put your tasks/steps.
• Emails: Email app on secondary, things you need to take care on primary. e.g. if email requires you to login to a site to do something, or you need to look up a document before you could reply.
• Misc: there are times you need eyes on stuff that's not work related. e.g. NBA, baby monitor, music player. I'd put them on secondary screen while trying to do easy tasks such as emails, digesting feeds on primary screen.

After I got a 27" ACD, which is large enough to have 2 applications laid side by side, it became more flexible.

• Coding/Web programming: resource and IDE on primary, results (webpage or simulator) on secondary.
• Misc: previous usages on either side of the primary screen, baby monitor on secondary.

The main principle is to keep your focus on the primary screen, while put something you need to look at after you finish each small tasks on the secondary one. If there's something you have to look at every few seconds, I'd suggest you put it side by side on the primary screen instead of on the secondary one and having to turn your head too frequently.

You do not say specific information about what you have to do with your computer in your work, so I would like to show you my current setup for gathering some ideas. In my work I read/write documents, data sheets and e-mails most of the time, but - as I am officially something like a software development manager - sometimes I have to write or review source codes as well.

I have two monitors, both of them with 1920x1200 resolution. The resolution is important because I use one monitor in a 'standing' position, using as an 1200x1920 monitor (and this setup does not work very well with an 1920x1080 resolution).

In this setup there is no 'primary' or 'secondary' monitor, both of them in front of me. My current task and the data I have to work determines which monitor I use. Some examples:

I use the 'standing' monitor with the 1200x1920 resolution for:

• browsing the web (most web sites does not scale well horizontally and I see much more content in the standing monitor)
• reading or writing documents (I can easily see a whole A4 page, sometimes even more)
• working with data sheets containing only a few columns (<15) but many rows (in Excel I see 80 rows together in this setup).

I use the other one with the 1920x1200 resolution for:

• dealing with my e-mails (with a horizontal layout in Outlook),
• working with data sheets containing many columns
• writing or reviewing source code (in an IDE with some other views open)

This setup works for me very well (I am using this setup for about 6 months and I feel the difference even though I have used multiple monitors in the past 4 years).

Ultimately, it boils down to why are 2 monitors more efficient than 1?

Reduction of switching windows

When you only have a few windows, it's easy to go between them, but it gets  
cumbersome as the number of windows start to grow.

With this in mind, here's how to achieve this:

Lay out the applications you want to see on the monitors at once. Do that for all the applications you use. After that, divide the windows to one monitor or the other.

Something I've found extremely helpful to supplement the effect of having 2 monitors are applications that do these:

• allow current window to be toggled always-on-top (e.g. always-on-top.exe)
• segment monitor into grids and hotkeys to force the application to be contained in that grid (e.g. WinSplit Revolution)

This gains much more flexibility to reduce switching between windows.