Recently, there was an article in New Scientist about this[1]. Basically, if you sit for more than 6 hours a day, one hour of exercise a day doesn't undo the damage.
The solution is to get up and move around often, i.e. every ~20 minutes or so.
Exercise is still good even if you stand/move around often. And standing all day also has its problems, like others have mentioned.
The problem with sitting for long periods of time, or remaining in any static position really, is that as muscles fatigue more stress is put on joints and bones. Having more muscle and strength helps significantly, but not all forms of exercise develops muscle and strength adaptations equally.
It would depend on the exercise. If you by "exercise" mean superflous human movement for the purpose of wasting excess energy, I would agree it doesn't do much to counter sitting the rest of the day, it's basically just a break from sitting.
If you instead mean methodical heavy barbell training for the purpose of invoking physiological adaptations in the form of increased muscle and strength, it would probably do a great deal to offset sitting for the rest of the day, especially coupled with the increased awareness and understanding of spinal positioning that comes with lifting weights.
Most of the time when people talk of "exercise", they mean the kind that don't do much for muscle and strength development (mainly the aerobic kind or light anaerobic work), but a lot of people actually do the kind that does.
"The solution is to get up and move around often, i.e. every ~20 minutes or so."
I agree. One method to force you to walk twice an hour is drinking a lot of water. This will keep your brain fit, you will be much less tired in the evening, when you leave for home. And - yes - you have to run to the bathroom quite often. 2-3 liters of water will do the job nicely.
That is also what my physician recommends (But don't try that with sweet or sweetened drinks).
I do this as well. I guess I should elaborate on my 8-12 hour days. It's rare now that I will sit in the chair for more than an hour at a time. Not only due to my awareness of the issues that it causes, but also because it just helps me clear my head to get up and go talk to some people, walk around the office, etc...
This should be done if you have a standing desk as well.
Clearing your head is important. Unfortunately, many people seem to forget that it is necessary. "The physiological effects of tiredness are well-known. You can turn a smart person into an idiot just by overworking him"[1].
Also: Getting out the door is good: Five minutes of "green exercise" turns out to be good for your mental health[2].
Exercise is still good, but it doesn't do magic if you live unhealthy the rest of the time.
(That being said, I wonder if the extreme types of workout many people promote is actually good, or if it does more damage than good in the long run. I guess some people believe that one extreme can out-weight another extreme.)
Quote: " "Jim" Fixx (April 23, 1932 – July 20, 1984) was the author of the 1977 best-selling book, The Complete Book of Running. He is credited with helping start America's fitness revolution, popularizing the sport of running and demonstrating the health benefits of regular jogging. Fixx died in 1984 at the age of 52."
The solution is to get up and move around often, i.e. every ~20 minutes or so.
Exercise is still good even if you stand/move around often. And standing all day also has its problems, like others have mentioned.
[1] http://www.newscientist.com/article/mg21829233.200-dont-take...
(edit: wording)