Boxee provide a great feature called App Box that allows uses to add and remove apps to the Applications Menu. The really great thing about App Box is that it allows the user to specify which Repositories to search for apps.

A repository is basically a directory of third-party applications. Once a repository has been added installing applications takes just one click. Also when the developer adds new applications to their repository they will automatically be available through the App Box.

Fuzz the Destroyer maintains a really nice list of available repositories on his site fuzzthed.com.

To add a repository:
Log into Boxee, navigate to App Box > Repositories > Add Repository and enter the URL of the repository you want to add (for example http://dir.nexthop.ie)