As aneeshep's answer explains, the key is creating an appropriate .desktop "launcher". But there's a simpler way than doing it by hand; in many cases, you may not even need to edit the .desktop file.

Solution: Use Ubuntu Tweak

• Ubuntu Tweak is a utility, which among other things, allows you to associate file types to be opened with a custom command. Behind the scenes, it creates a .desktop file which you can edit further for your needs, e.g. if you are using a command-line editor or program to open, etc.

In this how-to, we look at how to set up Nautilus to open .php files in the free Komodo Edit GUI text editor, which comes with a shell-installer that installs it in your home directory by default; the program/command is then /home/user/Komodo-Edit-7/bin/komodo

1. Install Ubuntu Tweak

• Add its PPA, update and install Ubuntu Tweak from the terminal with:

  
  
  

  
  
  sudo apt-add-repository ppa:tualatrix/ppa
  
  sudo apt-get update
  
  sudo apt-get install ubuntu-tweak
  
  

  
  
  

  Update: Check this question for updated instructions for newer Ubuntu releases

  
  
  
  
  
  • How do I install Ubuntu-Tweak?
  
  

2. Find the MIME description for your file extension

• Before using Ubuntu Tweak, we need to find the MIME description for the file extension we're interested in.



• Open Nautilus, find one of the files we want (here, .php), right-click on it and click on Properties:

  
  
  

  




• In the Properties window which comes up, note the text shown just after Type:; that's the MIME description we're looking for (here, "PHP Script"):

  
  
  

  

3. Add a custom program to open your filetype

• Start Ubuntu Tweak from the Dash, and click on the Admins tab on top; then click on the File Type Manager entry on the bottom:

  
  
  

  




• After the File Type Manager opens, click on All in the left sidebar, and uncheck the Only show filetypes... box at the bottom:

  
  
  

  




• Select any filetype on the right side, and begin typing the first few letters of the MIME description from Step 2 to automatically search and select your filetype:

  
  
  

  




• Double-click on your filetype, which is now selected, to edit its associated commands.

  
  
  
  
  
  • Click on Add, and in the Add Application window, expand the Custom Command option on the bottom
  
  
  • Type the command/program you want or use the Browse button to navigate to it and select it; here we have selected the Komodo-Edit editor from my home folder:
  
  
  
  
  

  

  
  
  
  
  
  • Click on Add, so the new command is now the default, and then click Close:
  
  
  
  
  

  




• PHP files will now open in Komodo by default, as seen in the Properties below; press the Reset button to go back to the default for that filetype: