I always thought the shakes/dry heaves were a result of completely taxing the muscle you worked of it's nutrients, in particular the carbs and lack of oxygen. I've also gotten the shakes and done the barf thing many times and it has always been a result of legs or back and in particular heavy squats, dead lifts, and leg presses. For the shakes there isn't much I could suggest that hasn't been suggested above. If you get nauseous I would suggest anything you can get your hands on with sugar in it. That's the only thing that can keep me from throwing up in the gym. Honey works good or a small packet of sugar. I know it defeats the purpose of the workout to a certain degree but I am NOT throwing up in front of people ever again haha.
glycogen depletion, yep. OMEGA and QT are saying its a good sign b/c using up all the glycogen stores means you've most likely worked the muscle hard enough to trigger an adaptive response from the muscle.
Be careful with swilling sugar though when you're very hot and depleted. It has been known to suddenly cause VERY loose bowels (ahem) with no warning.