There are a couple of different "parts" to the full MapWindow GIS offering. If you're a developer, you'll likely be interested in many of these. If you're just interested in using MapWindow to do GIS work (rather than development/programming) you'll probably just be interested in the first part.
a) MapWindow GIS Application
This is the full MapWindow application, the main offering. This provides a visual interface to work with GIS data, including geometry and attribute data, rasters and vectors, and performing spatial operations. The application ships with optional "plug-in" modules, such as a metadata editor, a GPS connectivity tool, and many other useful items.
b) GIS Tools Plug-in
This is an optional plug-in module for the MapWindow GIS application. This is included with the default package of tools from our downloads page. This allows you to perform spatial operations, including buffering and intersections, or to perform coordinate transformations and data conversions.
c) MapWinGIS ActiveX Control
This is the underlying map visualization component used in the MapWindow GIS application. If you're a software developer, this component can be used to quickly and easily add GIS capabilities to your software product.
d) MapWinGeoProc Library
This is a geoprocessing library for software developers. It provides the underlying functions accessible through the GIS Tools plug-in, as well as many other common GIS-related processing functions.
e) MapWinUtility Library
Available through the code repository, this is a library of common functionality needed when writing GIS-enabled software or plug-ins. The functions in this library are not GIS-specific (see MapWinGeoProc for those), but rather are common and reusable functions suited to any general programming task.
f) MapWindow.Web Library / Web Pages
Intended for use with ASP.Net, this tool is also called MapWindow 5.0 and is based around GDAL (Geospatial Data Abstraction Library) to provide a fully native and .NET library for web mapping.
g) MapWindow 3D / 6.0
The current bleeding edge MapWindow development, version 6.0 aims to be an ActiveX-free solution to eventually replace the MapWindow GIS 4.x series application for desktop use and mobile device use.