1. Open Source
Apache is open source and free, but you have to pay to Microsoft for IIS (directly or indirectly by purchasing Windows).
2. Platform Support
Apache can run on Linux (LAMP: Linux, Apache, MySQL, PHP) as well as on Windows (WAMP: Windows, Apache, MySQL, PHP). But, IIS runs only on Windows. Apache can run on UNIX, Mac OS X also.
3. Product Support
IIS is the preferred choice for the IT companies which uses Windows for development as they are assured to get the support from giant Microsoft but Apache support is available only from open source community, thats why its little hesitating for IT organizations to use it.
4. Technology Support
Apache is used with open-source technologies like PHP, Perl and Python, while IIS is specifically designed for Microsoft’s Active Server Pages.
5. Vulnerability to Threats
IIS works with Windows. There are lot of worms, trojans, spyware, malware, viruses for Windows as compared to Linux. So Apache seems to be secure in this respect if used with Linux.
6. Free / Cheaper Web Hosting
As compared to IIS, web-hosting on Apache Server is cheaper and you may get free also (with some restrictions like bandwidth, space etc.). In other words, a website created in PHP can be hosted cheaply as compared to a website created in ASP.NET.