Your post caught my eye as I was passing by doing some research on job sites.
In web development, like any with any software development situation there are many many trade offs.
I could go into listing them but I'm sure you could google for the pros and cons of either side.
I personally go for the LAMP setup, originally, through university I learnt primarily in .Net, as good as it is I still fell into an open source based business and have stuck with it ever since.
I feel open source suits development for the web far more than the closed source variants.
The server software is far more stable and has endless options, where the .Net solutions are closed off at what they give you.
If you look around at global trends towards government switching to open source systems you should be able to figure out that business will be soon to follow once they see the gains.
This will open up a lot of job opportunities in the future.
I personally prefer developing under linux for the web apps. Desktop apps I would pick C# with out a doubt. C#/.Net is much cleaner when dealing with huge code bases, and it deals with a lot of the mess PHP deals with constantly.
As much as I would like to move into .Net for web development I think I got sucked into all the open source propaganda.
Try them both, at your stage in learning the ropes you should be trying everything you can get your hands on and figuring out what you want to use.