I've read that the first Eco-Drive watches used supercaps, but they quickly realized that supercaps just didn't have enough capacity to be practical so they switched to rechargeable batteries. But I think the marketing types still want to refer to it as a capacitor so that they can claim that there are no batteries to replace.
Ed
I can tell you for sure that the original Seiko Kinetic - actually called the AGS (automatic generating system) - used a supercap, and it was an unmitigated disaster. Firstly, the energy recovery from body movement was crap - you had to be far more active than a wearer of a mechanical automatic. Secondly, the run time was only a few days.
Seiko painted themselves into a tight little corner with these. According to my jeweler, he had to return three out of every five he sold due to the inadequate energy harvesting. Here in the UK at least, the AGS disappeared from the shelves for a good three years.
All AGS and Kinetics have a power reserve indication, and here was a delicious conundrum. The voltage of the capacitor was proportional to the charge in it, so it was electronically simple to make a linear conversion from cap voltage to power reserve.
With the launch of the Kinetic, Seiko abandoned supercaps and went to a rechargeable cell. The UK service manager told me they had developed a tweak to the chemistry to make the voltage drop off more proportionately with charge - the exact opposite of what most battery manufacturers try to achieve. This was to allow a basic voltage sense circuit to provide the power reserve readout.
At last it worked - sort of. The power reserve indication was still a bit rubbish, showing fully charged until almost empty. Seiko refined this functionality over the following years. However, they had a problem with all the original AGS watches still in use. The supercaps went out of production so Seiko had to supply replacement rechargeable batteries to the trade, which were physically almost identical to the previous supercaps and dropped straight in with no tweak other than a change of insulator.
But the AGS was designed to use supercaps, and was launched before the decision to fit batteries. As such the power reserve indication was rendered unusable: it expected a nice linear voltage drop from 1.5V to tell it the charge level, but in reality the battery voltage changed far less. An AGS with a supercaps gave a reasonable indication of charge, with a run time of several days. An AGS with battery would have a power reserve in months, indicating "full" for all but the final week or two.
Basically the whole story is one of failure and compromise.
Interestingly, Seiko and Citizen both chose supercaps genuinely never expecting them to need changing. The thought was that a quartz watch is the lightest of light duty, and yet for reasons I don't understand, all of the supercaps eventually failed. I thought they would have lasted essentially forever unless their voltage or current ratings are exceeded.