Aparna,
I have a bias toward open source and thus my personal preference is a LAMP platform; however, you should know that either platform is supported. That being said, here is what tipped the scales for me to switch from
WIMP server (Windows,
IIS,
MySQL, PHP) to a LAMP. Your situation may be different so you should use your own good judgment as times have changed and I am writing about my experience from a couple of years ago.
Performance was my number one concern. I had difficulty getting a PHP accelerator working on the Windows server but I honestly do not remember how much real effort I put in to this and others seem to have been able to do so just fine. Secondarily, there seemed to me (at the time and this is a couple years ago) to be better support on the Moodle forums for LAMP related questions. My sense is that the number of users utilizing a Windows server has significantly increased.
The arguments against a LAMP server at the time were that it was one more thing for our techs to learn and they were much more familiar with Windows than Linux. The ability to support the chosen platform is important especially when there are problems. Another tidbit that I recall from the performance forum was that the issue may not have been so much the OS as the web server. I've heard that
WAMP is faster than WIMP. I've also heard that Linux does a better job at handling disk i/o.
As you can see there are numerous factors to consider. I do not think you would be overly limited by either OS. I would think in terms of identifying your priorities and then weighing out where you would anticipate the biggest problems. Hopefully my own experience (biased though it may be) will help to shed some light on your own situation. Feel free to continue to hash out your concerns, questions, etc.
Peace - Anthony