Fortunately, Motors are inductors. Therefore, simply dumping a capacitor across a motor should be a "good thing", although I wouldn't expect anything near the 100% efficiency you were calculating. However, I still think it is a good idea if only for the education.
A simple method would be to simply wire the cap in parallel with the fuel cell. This will give a minor boost, but you know you want something better than that.
Lets break the circuit into a few key components:
1) Fuel Cell power source
2) Really Big Capacitor
3) Boost Converter to charge #2
4) Switch to activate the system
It seems you already have #1 taken care of. Can you give us specs? Also, do you need to stop at the end of the race? Do you need to steer?
For #2, be sure that it is rated to handle some voltage. A lot of these super caps are rated for 2-5 Volts. Remember, your boost comes from the difference between the capacitors voltage and the fuel cell's voltage. If the fuel cell pumps out 3V, you'll want something rated a bit higher.
For #3, boost regulators are really cool circuits that convert a low voltage, high amperage source into a high voltage low amperage source. Since you apparently have a large start time to charge the cap, this is perfect. Google "Step Up" or "Boost" Regulator. Also, check out
www.linear.com and
www.national.com . Alternatively, search for my previous chiefdelphi post on boost regulators. I really love these guys.
For #4 you have a few options. The simplest one would be a single pole, double throw switch. One throw would connect the fuel cell, the other would connect the capacitor. This way, you would flip one switch and everything would come to life. Before this, the boost converter would be busy charging your cap.
Alternatively, you could use a nice MOSFET, a relay, or (my favorite) an SCR. However, they probably aren't worth the headache.
Good Luck!
Also, you might want to make sure this is legal.