I rely on the freedesktop utility xdg-open as it already has full integration with mime types and desktop files. I kind of pointed it a bit in this discussion about default programs.

So what I usually do is xdg-open, and if it doesn't call the program I want then I can switch it using mimeopen -a. In the case where my program isn't listed, I create a desktop file in ~/.local/share/applications, then update-desktop-database. Most of the time, this solves my issues, otherwise I can dive into adding my own mimetype in ~/.local/share/mime/application.