At work, I started using a ghetto standing desk with my lab PC about a month ago. At the beginning of the year, I got a new Dell tower and monitor (the U2311, which is really nice). The monitor box standing on top of a few plastic "project boxes" on top of a slightly higher than normal lab workbench is just the right height for my keyboard and trackball. The monitor sits on top of the Dell tower.
I like it, but the work I'm doing these days leads to some inefficiencies. I'm working a lot reading reams of documentation, connecting different things to various circuit boards, and running a logic analyzer. All of this stuff happens at the normal lab bench height. Because of this, I sit down about 25% of the time when working at my standing desk. That's OK, but it would be much nicer if I could raise the workbench up to the right height for my keyboard and trackball (it's about a 14" difference, I think).
The floor in the lab is 1 foot square industrial stick-on "tiles" (I think they're like linoleum). I don't use any kind of standing mat. My everyday shoes are 4 year old Adidas soccer shoes. The first week was a bit hard on my legs and back, I'd be stiff each morning, but it has gotten better. I still feel like I'm doing more physical work by standing (I've read it burns 3x the calories as sitting) but I'm not uncomfortable standing for 4 hours at a time.
The one thing I have noticed is that I'm more focused on my work when standing. Lately I'm writing C code for a PIC24f microcontroller. But I like to sit when I'm doing real hard core thinking, like when figuring out timing of interrupts or reading through assembly code. I'm not sure why this is. Having everything I work with up at the right height might help but I've not yet found the right sized cinder blocks laying around.
In my cube I still sit. My chair isn't fancy but it isn't too bad for comfort. At home I sit on a wooden chair when working on my desktop. My main motivation for trying the standing desk was that the chair I had in the lab was uncomfortable and rather than attempt to find a chair that would work, making a standing desk was quick and cheap.
So far I like it, although it does have downsides (my hardcore thinking, not everything being at the same level, etc). My coworkers think it's funny that I stand up but my boss has started pondering the idea of trying it since I've been using it successfully for a decent amount of time now.
If you're uncomfortable sitting all day, try a standing desk. It's all the rage on Hacker News ;)