If you really need to associate an extension with an application, then the file to change is registry.xml. In the past, this was done by directly editing the file. Now we have iliad-regutils (
iliad-regutils: Easy editing of the iLiad registry). No matter how you do this, modifying registry.xml is dangerous. At the very least, start out by making a copy of the file and test updating the copy.
Some "stand-alone" applications can be invoked directly from the content lister, without adding a registry entry, but if the application is supposed to work on a single file at a time then adding it to the registry is appropriate.