I'm thinking of setting up a server that'll host a PHP site loading data from mySQL.
How would I get the best performance(fast data transfer, high security and reliability):
What are the reasons for setting it up in with a Red Hat or Debian distro with Apache and mySQL rather than a MS Windows Server 2003 or MS Windows SQL Server? Is it worth relying on the open-source equipment or I would get the same results with Microsoft

If you are intending to run PHP and MySQL, then a Linux-based server would certainly perform well for you. However, a Microsoft Windows based server could perform just as well.

As for security, throughput and so-forth, it really does come down to you... or whomever sets-up the server for you. A properly configured server, with a good choice of network hardware and so-forth, can be "reliable, secure and fast" ... or not ... on any platform.

So, think about other considerations: are you familiar with Linux now, or is the person you intend to set-up and manage the site familiar with it? Do you own an MS license that's burning a hole in your pocket? Will the computer in question be expected to perform any other tasks? Do you contemplate running other web-oriented applications on the box which would push the decision one way or another?

I recommend that you take out a sheet of paper, draw a line down the middle of it, and make two lists: one for the Microsoft choice; the other for the Linux choice. Be honest with both lists. Try to be as thorough as you can be with both lists: give credit whereever credit is due, and be just as blunt about the negatives. Spend some serious time on it. Then decide.

If you would like to post your comparative list for user comments here, I'm sure that you would, indeed, get an objective and useful reply. (Along with a certain number of "cheerleader" responses, of course...) The more specific you can be, the better.

You can be assured that either of these two choices are "technically viable," so your decision really won't come down to "can it do the job?" That answer, in both cases, is "yes." What matters is the overall question of which type of system will integrate best with ... what you know now, what you are comfortable with now, and what else is currently in your shop. Either one is going to have some non-zero "cost of ownership," cost-of-maintenance, cost-of-employee-time and so on. Neither one is "free." The decision in any case is relatively low-risk, yet it is important that you inform yourself properly before making it.

As above, but seriously consider what you have most experience with. I would always go with linux because I can get it to do whatever I want to; I have lots of experience and feel totally at home. On the other hand I've not used windows for years and couldn't guarantee I'd know what to do.

So if you're new to linux but have vast windows experience, then stick to that. The only other thing to consider would be cost: if you don't have a windows license, remember you'll have to buy one. Linux or BSD are free

omg a SENSIBLE POST?!?!?!?! Last thing I was expecting what I clicked this thread

Now that I dragged myself back off that floor, who will be doing the most work administering this server? Use whatever that person feels most comfortable with. As has been said, any OS can be secure but on the same token, if not set up correctly any OS can be insecure also.

So aguess "it's all about the money"...
I knew about the cost issue between Linux and Windows, I was just wondering whether these Windows versions mentioned are worth of working with.
The server(thought about Apache) I want to setup will operate an e-shop that'll store the products' and customers' data in an mySQL DB and use through PHP or an e-shop engine.
To get to the point, all that'll make the difference is with which OS I'm more experienced and how much budget will be available?

Offtopic: Can someone tell me about a good, stable and secure e-shop engine?