The Joel Test
I just read an excellent article on the efficacy of programmers (or, the art of programming).
The other trouble is that it's so easy to get knocked out of the zone. Noise, phone calls, going out for lunch, having to drive 5 minutes to Starbucks for coffee, and interruptions by coworkers -- especially interruptions by coworkers -- all knock you out of the zone. If a coworker asks you a question, causing a 1 minute interruption, but this knocks you out of the zone badly enough that it takes you half an hour to get productive again, your overall productivity is in serious trouble. If you're in a noisy bullpen environment like the type that caffeinated dotcoms love to create, with marketing guys screaming on the phone next to programmers, your productivity will plunge as knowledge workers get interrupted time after time and never get into the zone.
With programmers, it's especially hard. Productivity depends on being able to juggle a lot of little details in short term memory all at once. Any kind of interruption can cause these details to come crashing down. When you resume work, you can't remember any of the details (like local variable names you were using, or where you were up to in implementing that search algorithm) and you have to keep looking these things up, which slows you down a lot until you get back up to speed.