Ease of Use
IIS is much easier for beginners as operators can maintain user-friendly screens and forms. Windows 2000, however, costs more than other operating systems like Linux, FreeBSD and Unix.

Straight Apache requires a huge learning curve to learn how to operate and manage. Everything is configured in text files very dark, and these settings are made by hand (although you can buy add-on utilities to enable entry of much of this information screens and forms.)

Security
The security model of IIS is one of the best ever designed, based as it is in NTFS (the security model of Windows NT and Windows 2000). This model is far superior to anything provided with Apache for non-Windows systems. Of course, in Windows, Apache can use NTFS as well.

Of course, IIS has been plagued by a series of vulnerabilities recently, and these are a concern. IIS is common to review at least every month, and the installation of a new service release (a collection of patches) twice a year. Most errors were made in Apache (before version 2) for a long time. Of course, with the launch of the second version of Apache you can expect a number of security holes and other surface – are a normal part of product life cycle.

Customizing
IIS does NOT have the equivalent of htaccess. Htaccess file in Apache is used to individually configure virtual sites (web sites) without restarting the web server. However, IIS has a very flexible configuration of ISAPI filters and other similar methods. Both methods (htaccess and ISAPI filters) are very hard to use  and for advanced webmasters.

Efficiency
According to several reports I’ve found lately IIS is more efficient than Apache. My own testing has led me to the conclusion of the performance of the two is more or less the same for static pages. PHP (server-side scripting common platform on Apache) tends to be more efficient than ASP (server side scripting system for IIS) according to many sources, although I have tested or speed.

Hardware Requirements
Both web server platforms large and small boxes of many different configurations require the same hardware. This is not surprising since the two platforms basically do the same.

When you configure Windows and IIS, it’s a good idea to remove the operating system functions that are not necessary. This reduces the size of the box you need (and safer).

Large farms
Microsoft has worked hard in the load balancing, so there are more options available for IIS and Windows 2000 for this than other operating systems. In fact, the group of Windows 2000 (the ability to run multiple servers using the same disks) is very advanced and makes disaster recovery a breeze.

Disaster Recovery
Backup solutions for IIS (those provided with Windows 2000) are surprisingly weak. There is no way to back up the metabase (all IIS configuration settings) from one computer and restore it on another (which makes it difficult for disaster recovery). On the other hand, Apache is only a matter of saving all text configuration files.

Language and other forms of support
IIS and Apache support CGI, SSI and Perl (ActivePerl on IIS is excellent). IIS natively supports ASP and I’m sure you could find PHP if you look (do not). Apache tends to PHP, although you can install something like ASP Chilisoft if desired.

CGI, SSI and PERL are performance hogs and security nightmares in both web platforms.

Stability
Both web platforms are rock solid stable. Apache servers which have remained so for over a year without a reboot, and  IIS servers have run for years with a restart is required only occasional service pack and security patch. Neither web platform (or OS for that matter) has even once crashed due to an error.

Operating System Integration
IIS and Windows 2000 is a more “integrated” environment of Apache, since IIS is targeted specifically for the operating system. This has the advantage that the GUI and controls of IIS look the same as any other tool in Windows.

Moreover, you can find Apache for almost any platform, including Lunix, Unix, BSD, and even things as OpenVMS. If you need to be able to move between platforms, then Apache is a great option.

Email
SMTP on IIS is primitive but functional. This is because it only serves to allow scripts and how to send email from the server. If you need additional assistance via email, it is expected that the use of Exchange or other mail system.

Apache does not support SMTP (sendmail), although a version is usually always on the target system. The email solution provides all the features – but be sure to check the settings to ensure that the system is not an open relay.

IIS SMTP module is configured through the standard input system Windows 2000, while Sendmail requires configuration file editing. IIS SMTP is absolutely trivial to maintain, Sendmail can be a challenge.

DNS
DNS in Windows 2000 is far, far superior to anything available on Unix or Linux. Bind (DNS for Unix and similar systems) has traditionally suffered from a large number of security vulnerabilities) and is very involved to maintain.
The DNS servers indicates the best solution is a dedicated DNS application box. These are inexpensive (for business), easy to configure and much safer than the version of Windows 2000 or Unix version.

Search Engines
No difference in the search engines referred between Apache and IIS (or any other web server, for that matter).