There are several kinds of file formats which you might prefer to always open in a specific Application. There's a way to natively set a file or set of files or all files to "Open With" one application. This seems to work uniformly on all formats, except when certain Applications override OS X associations.
To set one file to always open with one specific Application:
Select the desired file in Finder, and type Command + I. Under "Open With", choose the Application you want from the list, or choose "Other..." to browse for the file name.
To make a set of files always open with one specific Application:
Use the Spotlight search to find the files you would like to associate with one Application. Move them all to one folder, or go to the folder containing them all and select all of them together with your cursor. Type Command + I, and choose the Application you want under "Open With".
To make all files under one format open with one specific Application:
Select any file with the extension you would like to change to associate with one Application. Type Command + I, and choose the Application you want under "Open with", and this time, be sure to press the "Change All..." button.