When I stand at my desk, I'll do it until I feel uncomfortable/fatigued. When I sit at my desk, I stand when my back and legs get tight. It's that simple.
Before I made a big purchase decision, however, I figured I'd set one up using some spare furniture as stands just to make sure the idea worked for me.
For the first 30 minutes of standing, I wondered "wtf was I thinking?" After standing for an hour, I did get used to it.
After a couple of weeks, I realized a stand-only table was actuallly not a good idea for me. It wasn't so much related to fatigue (I do squats periodically to break the monotony and get the blood flowing), but I realized that for me, some work was just better done sitting.
My hand-eye coordination was never good to start with, and it was a little less precise (or maybe I'm a little less patient) when standing. I find that mouse-intensive work like manipulating an SVG in Inkscape or placing objects in a PowerPoint requires me to sit down.
I'm actually thankful I set up my temporary standing setup, because I realized that for a long term solution, I need either a sit-stand desk, or a something like a Varidesk (http://ca.varidesk.com/) or a Winston (http://www.lcdarms.com/winston-sit-stand-workstation.php).
Edit: see athenot's top-level comment.
I tried it at the store, and I was surprised at how smooth and fast the motor was, especially given the price.
http://iamnotaprogrammer.com/Ikea-Standing-desk-for-22-dolla...
[1] http://a.disquscdn.com/uploads/mediaembed/images/376/3321/or...
I ended up ordering a base [0], and bolted on an 8'x3' melamine sheet from Home Depot [1] (they chopped off 1 foot, lengthwise, in the store).
Three extra things I had to do to make this work:
1.) I had read that unsupported melamine will sag. I bought a thin steel beam [2] to add support in the middle. They chopped it in half in-store and it fits nicely between the base and the top.
2.) Iron-on edge banding [3] will "finish" the sides.
3.) I failed a couple times at getting the adjustment console attached to the bottom of the table. You have to pre-drill some holes near the width of your screw, and you have to make sure your screw isn't so long that it comes out the other side(!). The diameter of the head matters too. You'll see why when you see the console. Order the base first, and when you go to Home Depot take the console thing with you to find the appropriate screws.
Now I have a sturdy, 8 foot(!) adjustable desk. If it starts sagging in a couple years (and it very well might), I can spend $25 for a new top. I should point out that I'm not that good at building things, and this wasn't too bad. The hardest part was getting an 8'x3' board from Home Depot back to my house (they'll rent you a truck for like $20 if you need it).
At the same time, I switched my chair to a red exercise ball ($30 at Target). I think this was a really good idea (even if one doesn't change their desk), if only for the fact that when I'm standing on a conference call I have this giant ball to mess around with, now. Others might be able to speak to health benefits.
I also had to ease into standing, like others have mentioned. I started with standing for two half-hour chunks a day, for maybe three days, then bumped it up to two 1-hour chunks a day, etc. Now I'm at about two 3-hour stints a day, which is probably where I'll stay.
In three months with this setup, my back feels 10 years younger and I'm much better at standing (both the state of standing as well as standing up from a sitting position*), getting out of bed and bending down to pick stuff up (most notably shoes and small family members). I also walk taller and have better posture.
[0] http://www.thehumansolution.com/uplift-900-electric-sit-stan...
[1] http://www.homedepot.com/p/Unbranded-Melamine-White-Panel-Co...
[2] http://www.homedepot.com/p/Everbilt-1-in-x-72-in-Plain-Steel...
[3] http://www.homedepot.com/p/Unbranded-13-16-in-x-250-ft-White...