The advantages of upgrading the server that hosts your 
existing IIS Web sites and applications to IIS 6.0 include 
the following: 

• Reduces the time required to deploy IIS 6.0. Upgrading 
requires minimal user interaction.
 
• Reduces possible configuration errors. Because the 
majority of the current operating system, IIS, and Web site 
configuration settings are retained during upgrade, fewer 
configuration errors result.
 

The disadvantages of upgrading the server that hosts your 
existing IIS Web sites and applications to IIS 6.0 include 
the following:

• Retains previous versions of software. The upgrade 
process upgrades only software components identified by 
Microsoft® Windows® Server 2003, Standard Edition; Windows® 
Server 2003, Enterprise Edition; and Windows® Server 2003, 
Web Edition. Any other installed software components, such 
as applications or application dynamic-link libraries 
(DLLs), remain unchanged. 
 
• Retains the previous registry configuration. The upgrade 
process makes the appropriate modifications to the registry 
entries identified by Windows Server 2003. Registry entries 
are created by an application as it is installed, but are 
not removed when the application is removed. Cumulatively, 
these registry entries consume disk storage and can make 
troubleshooting registry-related problems more difficult 
because the unused registry entries can have similar naming 
conventions to active registry entries.

Advantages:
1. You can create multiple websites in IIS6 compared to 
IIS5.x .In IIS5.x, we can create only one website and under 
the website, multiple virtual directories.