If you've been looking in the various forums and newsgroups devoted to webmastering, You can see lot of debate is about web servers. More precisely, which one is better: Apache or Internet Information Server (IIS). You can see these both web server platforms are really functionally equivalent.
Ease of Use:
IIS is much easier for the novice as operators can maintain it from easy-to-use screens and forms. Windows 2000, on the other hand, costs a lot more than other operating systems such as Linux, FreeBSD and Unix.
Straight Apache requires a huge learning curve to learn how to operate and administer. Everything is configured in extremely obscure text files, and these configurations are done by hand (although you can purchase add-on utilities to enable entry of much of this information from screens and forms.)
Security:
The security model of IIS is one of the best ever designed, based as it is upon NTFS (the security model of Windows NT and Windows 2000). This model is far superior to the anything provided with Apache for non-Windows systems. Of course, on Windows, Apache can use NTFS as well.
Of course, IIS has been plagued with a number of vulnerabilities lately, and these are a concern. It's common to patch IIS at least monthly, and to install a new service release (a collection of patches) twice a year. Most of the bugs were worked out of Apache (prior to version 2) long ago. Of course, with the release of version two of Apache you can expect a number of security and other flaws to surface - these are a normal part of a product's life cycle.
Customization:
IIS does NOT have the equivalent of HTACCESS. The HTACCESS file in Apache is used to individually configure virtual sites (web sites) without restarting the web server. However, on IIS you have a very flexible method of configuration with ISAPI filters and other similar methods. Both methods (HTACCESS and ISAPI filters) are very obscure and for advanced webmasters.
Efficiency:
According to several reports that the IIS is more efficient than Apache. But as we check for the performance of the two is roughly the same for static pages. You can see that the PHP (the server side scripting platform common on Apache) tends to be more efficient than ASP (the server side scripting system for IIS) according to many sources.
Operating System Integration:
IIS and Windows 2000 is a more "integrated" environment than Apache, since IIS is targeted specifically for the operating system. This has the advantage that the GUI and controls of IIS look and feel the same as every other tool on Windows.
On the 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.
Email:
SMTP on IIS is primitive but functional. This is because it is only provided to allow scripts and such to send email from the 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 the target system. The provided email solution is full featured - but you must be very sure to check the configuration to be sure your system is not an open relay.
The IIS SMTP module is configured through the standard Windows 2000 entry system, while Sendmail requires configuration file editing. IIS SMTP is absolutely trivial to maintain; Sendmail can be a challenge.
DNS:
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.
DNS servers indicate the best solution is a dedicated DNS application box. These are inexpensive (for a business), easy-to-configure and much more secure than either the Windows 2000 version or the Unix version.
Search Engines:
There is NO difference as far as search engines are concerned between Apache and IIS (or any other web server, for that matter).