sitting on a one of those work out balls? Atleast that would engage your core muscles?

Here's a good article on the dangers of prolonged sitting and some ways to combat them. There's probably no one position -- sitting or standing -- that's good for the body to stay stationary in for hours at a time. When I researched kneeling desks and other unusual configurations, people generally reported that they felt great at first, but after a while they just developed pain in new places. So the key seems to be to change positions and move your muscles around as much as possible. There are "destabilizing cushions" (mentioned at that article) that you can put on your chair to keep your muscles somewhat awake and involved. But the most important (and cheapest) thing appears to be making sure you get up and move around and work your muscles and joints as often as possible.

Take your office outside?

Barring that, I highly recommend an Ergonomic Kneeling chair.

Barring any change in seating, getting up and opening up your hip flexors with a few stretches every hour or so does wonders.

I started to work at a standing desk in February. I was experiencing very mild lower back issues and I'm quite young so I wanted to be pro-active about it. Before standing up, I gave the exercise ball a try but it was not natural enough for me. I would only be able to sit on the exercise ball for around 30 minutes to an hour at first while I was able to stand up for a ratio of about 3 hours of standing and 1 hour of sitting twice a day since the beginning.

If standing up is not an option, I would definitely try a kneeling chair, it seems more natural than the exercise ball to me. It would also fix your problem and prop you up the missing 6 inches.

If there is a way to raise the cubicle walls just around your area, maybe your co-workers wouldn't feel their privacy was being invaded. Or find a job where a) the employer isn't too cheap to buy full-height cubicles and b) the boss isn't a tyrant.

I sit on a tall wooden stool at work, so I at least have to keep my back straight.

try the Squat position interspersed with kneeling and seated positions. The advice is to move as much as possible and to remain inert as little as possible. Standing will elevate metabolic rate n-tuple times above seated/kneeling posture...

I work at a place that has standing desks!!! Freaking Rocks!!!

Don't hate your boss too much, not wearing shoes is a major workplace liability. Mention that you're considering it and ask if it's allowed. Saying no is something that makes them look bad nowadays, since this is a health issue.

in the meantime, while you look for alternatives, you could try to sit cross legged in your existing chair, yogi style. for some reason, this tends to straighten my posture right out and makes chair sitting seem tolerable for longer periods. I learned this one on Amtrak.

I've worked in a store for a couple of years,which is all about standing. Reading all stuff about standing desks,I find it odd that nobody's mentioning varicose veins in the leg. 'cause that's definitely a downside of standing.

There are such things as kneeling chairs (http://en.wikipedia.org/wiki/Kneeling_chair). They are mainly used to improve posture and alleviate back pain associated with long periods of sitting but it may be worth considering. Loads of sources - Google is your friend (for a change!)