How does one decide which font to use while designing the logo of a corporate site?
That's like asking, "how does one decide what type of website to design for a corporate site?". It depends on many factors such as colors being used for the design, the mood/emotion you want to communicate, the desires/preferences of the corporation, etc, etc, etc.
Folks go to school for four years to just learn this. :o) However, I think if you contrast/compare with similar corporations out there, you can come up with a decent logo.