Jose,
You can charge a capacitor to any voltage. It only becomes a problem when you are trying to charge it to a voltage that is higher than it's rating. You can use the 1 volt fuel cell to power a voltage multiplier much like the article in your post above. Maxim has a few handy ICs that are designed for these applications. If your motor is rated for 6 volts then charge a cap up to 6 volts and then dump it into the motor. 6 volt capacitors are generally smaller in size than a 16 or 25 volt cap but you can still use the higher rated cap charged to 6 volts.
Capacitors are funny little beasts. When charging, the voltage starts out very small and rises exponentially until max charge is reached. This takes about 6 time constants to achieve, where t=R*C. The voltage that appears at the terminals will be V(cap) =Vin(1 - e^{-t/RC}) if you are solving for time. The charge current is the inverse of this. Current is maximum at the start of charge and falls off to zero when a cap is fully charged. In discharge both current and voltage are reversed. The cap will deliver max voltage and current at the start of discharge both falling to zero at the end of discharge, again as an exponential function. this link has a good curve and explanation
http://hyperphysics.phy-astr.gsu.edu...ic/capchg.html
The 555 timer is a special circuit that uses the function of RC timing (cap charge/discharge) to perform timing functions. If you were to use the same cap for both motor function and timing, that would be pretty cool.
Once you take a look at the charge discharge curves, you will start to get a feel for the action of the cap in your application. During charge you can have one time constant that is determined by the charging circuit series resistance and chosen so that you do not exceed the fuel cell 500 ma max current. On the discharge side, your time constant is now determined by the series resistance of the motor and wires. The discharge constant will be very short due to the low series resistance of the motor. Say you were using a motor like the Fisher-Price motor. It has a resistance of about 0.12 ohms. With a bank of caps rated at 0.5 farad the bank would be fully discharged in 6 time constants or 6*0.5*0.12=.36 seconds. But it would only produce some useful current for perhaps 1 or 2 time constants. Remember that the using the equation above, one time constant will discharge the cap to 37% of it's fully charged value. So in 0.06 seconds the voltage in the cap will be down to 2.2 volts but the current will be as high as 50 amps. With all things considered, you might find that in 0.06 seconds, you may have not been able to transfer enough current to get the motor turning. Only experimentation will tell, different motors will have different resistance and power curves. Good luck.
As to the flywheel, all you have to do is have a pulley attached to your drive wheels that pivots against the flywheel. When the race starts, just allow the pulley to fall against the flywheel to conduct the flywheel energy to the drive wheels. A spring would help do that as well as having a grippy surface on the pulley. Then use the fuel cell to drive a motor that spins up the flywheel.