ASP.NET allows you to access .NET technologies from your IIS applications. There are special considerations for configuring ASP.NET applications on different versions of an IIS server:
The aspnet_wp.exe worker process does not exist when using IIS 6.0 worker process isolation mode because the ASP.NET pages are executed within the w3wp.exe process. See New System Architecture for more information about IIS 6.0 process isolation.
The ASP.NET worker process runs under the special Windows user identity, ASPNET, that is created when ASP.NET is installed. The userName and password attributes of the <PROCESSMODEL> configuration tag allow you to specify a different user identity for the worker process. See the topic titled Configuring ASP.NET Process Identity in the ASP.NET SDK for more info. Also, see the topic titled ASP.NET Required Access Control Lists (ACLs) for info on required access rights that are required by ASP.NET.
ASP.NET security takes over after IIS security checks are finished. Most Web developers will set IIS up to allow anonymous users then use the ASP.NET authentication and authorization security schemes: Forms authentication, Passport authentication, Windows authentication.
There are framework version dependency considerations when building ASP.NET applications. Most applications that are build on version 1.0 might not be fully compatible with IIS 6.0. See www.GotDotNet.com for more information about compatibility considerations and version changes.
Platforms: Windows XP with IIS 5.1 and .NET Frameworks installed, Windows Server 2003 family with IIS 6.0 installed and ASP.NET enabled
Source: Microsoft MSDN