Both GNOME and KDE are a lot more than just window managers. They dictate a look and feel. You can offer that same look and feel with your application by using their related development environment. In the case of KDE, the development environment is Qt. In the case of GNOME, it is GTK+. Again, the choice is really a combination of personal preference and compatibility with other applications.
The compatibility issue isn't about whether you can run GTK-based and Qt-based applications on the same system (you can). It is strictly look-and-feel, again. For example, while the GIMP, a bitmap graphics manipulation program similar to Adobe's PhotoShop, is based on GTK, it runs perfectly under KDE.
As always, the radio program will discuss these concepts in more detail and then go on to talk about recent happenings in the Linux community. Tune in for details.