Compared to Windows, there are really very few unique advantages and disadvantages to using Linux Web hosting services. Generally, any popular Web application can be run on either platform. Both platforms can be remotely administered in very similar ways.
Overall, I would choose the platform that you (and your developers) are more familiar with. You'll find that a much more significant differentiating factor is the way the ISP has implemented the hosting platform -- how it performs monitoring, maintenance, what applications it allows you to run, etc.
This was first published in September 2003