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Language and other support
IIS and Apache both support CGI, SSI and PERL (ActivePerl on IIS is excellent). IIS natively supports ASP and I'm sure you could find PHP if you looked (I have not). Apache tends towards PHP, although you can install something like Chilisoft ASP if you want.
CGI, SSI and PERL are performance hogs and security nightmares in both web platforms.
Both web platforms are rock solid stable. I have run apache servers which have stayed up for longer than a year without a reboot, and my IIS servers have run for years with only rebooting required is occasional service pack and security patch. Neither web platform (or OS for that matter) has even once crashed due to a bug.
Operating System Integration
IIS and Windows 2000 is a more "integrated" environment than Apache, since IIS is targeted specifically for operating system. This has advantage that GUI and controls of IIS look and feel same as every other tool on Windows.
On other hand, you can find Apache for just about any platform, including Lunix, Unix, BSD, and even such things as OpenVMS. If you need to be able to move between platforms, then Apache is a great choice.
SMTP on IIS is primitive but functional. This is because it is only provided to allow scripts and such to send email from server. If you need additional email support, you are expected to use Exchange or some other email system.
Apache does not support SMTP (sendmail), although a version is usually provided on target system. The provided email solution is full featured - but you must be very sure to check configuration to be sure your system is not an open relay.
The IIS SMTP module is configured through standard Windows 2000 entry system, while Sendmail requires configuration file editing. IIS SMTP is absolutely trivial to maintain; Sendmail can be a challenge.
DNS on Windows 2000 is far, far superior to anything available on Unix or Linux. Bind (he DNS for Unix and similar systems) has traditionally suffered from a huge number of security vulnerabilities) and is very involved to maintain.
My own experience with DNS servers indicates best solution is a dedicated DNS application box. These are inexpensive (for a business), easy-to-configure and much more secure than either Windows 2000 version or Unix version.
There is NO difference as far as search engines are concerned between Apache and IIS (or any other web server, for that matter).
I'm sure I could write for hours and hours about this subject (and perhaps I will in an article on my own web site). Basically, IIS and Apache do same thing. They have a vastly different design philosophy, however, and underlying operating systems have even wider differences.
My experience is that Linux and Unix people prefer apache, and windows people prefer IIS.
To me, choice of webserver really comes down to "what are you and your group comfortable with?" If your experience is with apache, linux or unix, then you probably want to stick with Apache. If your experience is with Windows, then you will probably be uncomfortable with Apache.
I've used both (and several others) and quite frankly, to me, it does not matter. Drop me on a server running apache or IIS, and I will feel at home.
Richard Lowe Jr. is the webmaster of Internet Tips And Secrets at http://www.internet-tips.net - Visit our website any time to read over 1,000 complete FREE articles about how to improve your internet profits, enjoyment and knowledge.