I did more research and learned that my original plan was a lot more complicated than it needed to be. I found that I could use frequency shift keying (FSK) like the one I saw here and here which are both for the iPhone and should be usable for other devices with little or no modification. I'm currently researching how to do it directly using C# code on the Netduino which isn't in the scope of this site anymore so I have to find help elsewhere.
Anyway, thanks to both Joe and Chris Stratton for providing answers. I'm sorry if I had to unset Joe's answer for my question as it does not apply anymore. Both answers are still very informative on my side though so thanks a lot. I'd probably make use of them in another project.
I saw this answer and glanced at my watch, it just so happens to function in the way you describe. There's a large half-disc pendulum inside which presumably is used to collect the kinetic energy. It can run for about let's say one day If I walk about 2-4 miles a day. If I move throughout, indefinitely, but then, watches require very little power to begin with.
Energy Storage
How much energy you can store only depends on your capacitors and batteries, etc, it's not inherent to the the energy generation method you want to use.
Other Devices
I don't see why you would look at it this way as mentioned before. Decide on what you want to use kinetic energy to power and then do a few basic calculations based solely on first principles, assuming 100% efficiency of kinetic energy -> chemical / electrical energy and you'll quickly see what's doable and what's not. As a general guide, microWatts, up to a maximum of say a few milliWatt is probably all you can do (this very much depends on the type of physical activity you're using, more strenuous activites could very much reach into Watts)
Schematics
I can't give you one, but I can tell you the design is very simple. Take the pendulum in my watch mentioned earlier(here's a picture of one from your article):
While I can't specify exactly how thing's work internally, what I do know is this:
"Electromagnetic induction is the production of an electric current across a conductor moving through a magnetic field"
After reading the provided article, the pendulum is used to spin a pinion(visible in the picture) - just a small gear, which in turn drives an electric generator(which has been documented plenty). Anyway, you're likely to get an AC voltage from the electric generator. You can use perhaps a bridge rectifier, maybe a voltage regulator as well and store this in the energy storage device of your choice.
Finally
Like I said before, decide on what you want to power first, that's the only way you're going to be able to do this properly. Make an upper maximum required power for the circuit you want to power and proceed from there. Feel free to ask for any more help but based on the information so far, this is all I can do.
Best Answer
The circuit shown using the MAX1675 is a boost regulator producing 3.3V and if you look at the data sheet, it is capable of being modified to produce up to 5.5V. Page 6 says that if the FB pin is grounded, the output will be 5V.
This is dependent on sufficient voltage from the piezo device and loading conditions on the output being reasonable and compatible with the energy you can take from the piezo.