You are encouraged to visit the original author of this (in case of updates) but I provide it here largely for my own benefit -- or in case it disappears as many items on the web do.

DotNetNuke Upgrade Procedure

• If you use 3rd party modules, check the developers site for compatibility and necessary updates. 
• Backup your DNN database and installation folder in file system, where DotNetNuke resides 
• create a copy of your web.config file
• download the appropriate package from www.DotNetNuke.com
  • Source= core framework with souce code and all current core module versions (install versions, if available)
  • Installation = same as Source, but without source code 
  • Upgrade = core framework without source or module packages
• Check the forums at DotNetNuke.com for issues reported
• Stop your web site  in IIS
• If upgrading from DNN 3 to DNN 4:
  • delete all .vb files in the DNN installation directory and subfolders
  • delete all DotNetNuke dll files in folder /bin löschen (Attention: not files of any 3rd party modules!)
  • use install instead of upgrade package 
• Unzip the package into the installation directory, make sure, that existing files with same name get replaces (pay attention: source version of DNN 4 has an addition root level with library and website folders, website constains the runtime files.
• rename release.config into web.config
• from previously used web.config copy the following entried into the new web.config
  • both datenbase connection strings 
  • both encryption keys 
  • in section SQLDataprovider copy keys
    • DataBaseOwner
    • ObjectQualifier
• check folder /install/modules for module packages, you do not want to install/upgrade. Since DNN 4.4.0, modules with appendix .resources don't get installed, but are made available for quick installation via menu item Host :: Module Definitions.
• If upgrading from DNN 3 to DNN 4 alter IIS settings for your Web Site or virtual directory
  • switch ASP.Net version from 1.1 to 2.0 
  • make sure, that applications using ASP.Net 1.1 do not share an app pool with ASP.Net 2.0 applications. If necessary, create a new pool. 
• start your web site in IIS 
• call your web site in your browser, this will start upgrade process and module installation 
• install additional modules either using menu item Module Definitions or copy the packages to /install/module and call /install/install.aspx?mode=installResources
• install updates language pack(s) either interactively using Host :: Languages menu item or copy the packages to /install/language and call /install/install.aspx?mode=installResources