You can create extensions for DotSpatial or you can create your own application using DotSpatial controls. The following factors may influence you to pick one over the other:

Extension

• You'd like other people that are using Mapwindow 6 or other DotSpatial-based projects to be able to discover your contribution.
• You want to focus on your business logic, interacting with the map, etc. and not on creating an application.
• You're just getting started.

Application

• Your app won't look anything like the standard Legend and Map layout.
• You wan to embed GIS functionality within a custom application
• You need full control.

Note that you can distribute an application with your extension "built in" by adding it to the Application Extensions folder.