* the changeover from DNN 3.x to DNN 4.x - DNN 3.x used asp.net 1.1, whereas DNN 4.x and above require asp.net 2.0
* editions prior to 4.6.2 - Prior to 4.6.2 site admins had to manually merge a number of key fields in web.config such as the machinekey and both connection strings. With 4.6.2 DotNetNuke introduced functionality known as xmlmerge which automatically does the web.config merging on your behalf.
* DotNetNuke 5.2 - this version introduced the requirement for SQL 2005 and .net 3.5 SP1
* All versions prior to 4.6.2 require manual merge of the web.config. From 4.6.2 on when an upgrade package is overlaid over an existing instance, DotNetNuke will automatically merge the necessary web.config changes.
* 3.02.02 - 4.03.07 - please refer to the Detailed installation guide "Upgrade to DotNetNuke 4.x chapter" - http://www.dotnetnuke.com/LinkClick.aspx?fileticket=gOZGbvrVKJw%3d&tabid=478&mid=857
To run a manual merge of your web.config you need to use a comparison tool. Winmerge is a good free opensource tool for this. A well regarded commerical tool is Beyond compare