Just encountered a new window fault myself on my Jan '05 GT 1.9 JTD, having experienced the inch-by-inch stop/start motion on the driver-side window on a pretty regular basis over the past 2 1/2 years I've had the car. (That fault, as stated elsewhere, has always been easily fixed by holding down the switch for the driver's window for 10 seconds, but only while the car is stationary, interestingly enough.)
Today's fault was a new one on me though and almost certainly a computer/software bug. I'd unlocked the car with the key fob/remote, and then opened the windows half-way by pressing down the same unlock button on the fob. On starting the car 5 minutes later and driving off I realised that neither driver-side nor passenger-side windows worked anymore. They didn't move up or down, no noise, no reaction, switching the engine on and off didn't help, and the window didn't budge down an inch when opening the door either. Interestingly, the odometer started flashing from the point where I tried to use the window switches. Everything else I checked, electrical and mechanical, seemed to work fine.
Had to pull the power at the battery, left the leads off for 3 minutes, came back and reconnected the battery and - hey presto - all working again. On opening and closing the car doors (driver side and passenger side) the windows wound themselves up all the way, even without starting the engine.
Pesky software! Just wanted to contribute that one as I couldn't see that exact problem or solution referenced elsewhere. (FYI: winding down the windows from the key fob/remote previously worked fine for me and didn't disable the window switches, not sure what I did differently this time.)