There are nine folders in the downloaded zip file for HTML Agility Pack:
The different versions are compiled against different .NET framework versions. Some frameworks, such as the WinRT or the Silverlight frameworks, have more limited functionality or require slightly different (and often slower) approaches to implement the features of the component you're using.
You will want to use the HTML Agility Pack version that best matches your applications. So:
When you want to use the component with multiple apps, choose the lowest common denominator.