I have to develop an application for windows that will enable controlling the mouse through web cam by recognizing hand gestures. I will be using vc++ 2008 for development. But
A quick way to put it: the performance difference between the native API and .Net can be compensated for by buying a more expensive processor. You would pay somewhere between $1 and $100 more, with $10 being a reasonable estimate - per CPU of course. So, if you expect more than a million users, do choose the native API. If you expect to use it on 2-3 demo PCs, it really doesn't matter at all.