I created a workstation that allowed my screen to be at eye height and keyboard/mouse to be at the right height for my elbows to be at right-angles. That was by far the most comfortable position to stand and type/mouse from. Later on I found having the mouse higher actually helped too with arm ache.
As for how long I could stand for, the first week was not a problem. I was doing 8am-1pm followed by 30 minutes sitting down, and then 1:30pm-6pm without a break other than a walk to the toilet occasionally.
From week two my legs really started to ache from the kneee down, I found myself leaning on the desk to take away the pressure. Investigating why this was happening I found it is to do with keeping your legs stationary as the muscles can cramp or just go stiff. The solution is to keep moving so a cheap manual treadmill should do the trick. The alternative of taking frequent breaks doesn't work as it breaks concentration.
If you have to do this for a couple of weeks then you should be able to cope, if you want to make a "change for life" then come up with some way to keep moving while working.
For those who do sit down all day and don't have back problems a word of caution. Sitting all day makes your lower back very stiff, but you won't notice this until you try to do something and hurt yourself. It may be a lifting task that an unstiff back could cope with. Taking time to exercise and stretch can save you such a disaster, I am healing well now, but still get twinges and have to be carefull.
That is the right caution, but the wrong reason. A stiff lower back (lumbar) is desirable. You want to be mobile at your hips, and upper back (thoracic) and have the ability to keep the lumbar stable. When you lift something your lumbar spine should be immobile.
You are correct that there are problems with sitting but it is that typically your lumbar is rounded so that you are weakening and stretching it all day long making it difficult to maintain proper posture when you lift something from the ground.
A quick rule of thumb for mobility: Ankles (mobile), Knees (immobile), Hips (mobile), Lumbar (immobile) and Thoracic (mobile). Stuart McGill is a great resource for learning about proper back mechanics.
Oh, BTW, I use a stand up desk and love it.
One of the best things I've found about standing is that it keeps me more alert and awake throughout the day. This is by far the most immediate plus, for me.
The important thing to remember is to keep moving - change your position often. I have considered the manual treadmill route, but I'm a little concerned my co-workers wouldn't appreciate the noise. Walking in place seems to work just fine - but does earn me some odd looks.
Other possibly relevant factors: Switched to dvorak about 10 years ago. I'm in athletic shape and maintain a healthfull diet.
I usually have a dead tree format book going, and take occasional breaks during the day to read, cook, exercise, take a walk, etc.
Footwear makes a big difference. Minimal slippers were best. Anything with arch support makes my feet hurt after a few hours.
1) sitting down at my home office (nice wood furniture and decor the whole works)
2) standing at my work office (ugly but very functional perma-temporary standing desk)
... and don't have any problems at all. I type as long as needed, etc. However, I never stand still for more than a few seconds. (This seems to be a built-in feature of me, rather than anything I do intentionally.)
For the first few days my feet hurt after standing for an hour or so, however I did find that I felt more energetic throughout the day. I did have an odd feeling of being unsettled the first day, but after that I found it easier to focus, especially with the extra energy.
By the fifth day the pain in my feet was significantly reduced. This week I've returned to my (fairly) ergonomic sitting desk setup and I've noticed posture issues and some discomfort in my lower back.
My experience was that alternating short periods on a tall stool with standing provided the most comfort. The paper, "The benefits of sitting and standing to work" (http://www.ergomotion.com.au/images/PDF/HFESA%20paper%202008...), references a study in which 30 full-time bank tellers came to the same conclusion. Using a chef's mat can also provide some comfort for your feet.
I tend to stand around half the time at work, which comes to something like three-four hours on the average day. If I have just done a long run or bike ride I might sit for the entire day as my legs and back will already be fatigued.
The thing that makes me sit is aching feet. I suppose standing for a long time makes bodily fluids assemble in the lower legs, so after a while the feet start to feel a bit swollen and the heels get sore from having all the weight on them. This is alleviated by switching around from one leg to the other, but after a couple of hours I need to sit for a while (this is the reason a desk must be stand OR sit and not fixed to standing-only - you need the ability to adjust according to the situation.)