Can you pull up the context menu in a Stack (e.g., Downloads)?
If the application you want to open the program in is in your Dock, you can drag the file icon from the Stack and drop it on the application icon.

Alternately, command clicking on the file in the Stack will open a Finder window with that file already selected. You would still need to control-click it and open it, but it cuts out a few steps.

Sadly, there does not appear to be a way to make the context menu appear in a Stack.