Programmatically/Script-atically changing the default Open-With setting
This is doable, but probably isn't as straightforward as you might think.  You'll need to get very familiar with Uniform Type Identifiers.  Look at Wikipedia's Uniform Type Identifier page.

OS X stores information on preferred file associations in a preference file with the name com.apple.LaunchServices.plist.  Before you go try to find and modify that file, I suggest you familiarize yourself with OS X's domain hierarchy for defaults (a.k.a. "settings").  A decent article on this can be found here. (Disclaimer: they seem to be selling something on that site. I don't know what it is and have no association with them, the explanation is just a good one.)

Now that you know all about defaults and UTIs (er, not the medical kind), now we can talk about setting file associations from a script/command line.

First, you'll need to know the proper way to identify the files for which you want to make an association.  

Remember how I said UTIs were important?  There are multiple ways to identify a file.  It depends on if the type has been formally declared on your system or not.  For example, decent text editors like TextMate or TextWrangler will add quite a few type declarations to the type hierarchy when you use them on your system.  If, however, you don't have those applications, you may not have those types declared.

OK, enough talk.  Examples:

Get the UTI for a file:

$ mdls myFile.xml
...
kMDItemContentType             = "public.xml"
kMDItemContentTypeTree         = (
    "public.xml",
    "public.text",
    "public.data",
    "public.item",
    "public.content"
)
...


Ok, cool.  An explicit content type we can use.  Write that down somewhere.

$ mdls myFile.myExtn
...
kMDItemContentType             = "dyn.ah62d4rv4ge8048pftb4g6"
kMDItemContentTypeTree         = (
    "public.data",
    "public.item"
)
...


Oops.  OS X doesn't know about ".myExtn" files.  So, it created a dynamic UTI that we can't use for anything.  And the parent types are too generic to be useful.

Now that we know what our files are, lets look at the LaunchServices.plist file and see what we can do:

$defaults read com.apple.LaunchServices
{
    ...
    LSHandlers =     (
                {
            LSHandlerContentType = "public.html";
            LSHandlerRoleAll = "com.apple.safari";
            LSHandlerRoleViewer = "com.google.chrome";
        },
    ...
                {
            LSHandlerContentTag = myExtn;
            LSHandlerContentTagClass = "public.filename-extension";
            LSHandlerRoleAll = "com.macromates.textmate";
        },
    ...
    );
    ...
}


So, when you have a "good" content type to use, the first construct is better.  Otherwise the other construct.  Note, there are other constructs in that file, but they aren't relevant to what you asked.  Just know they are there when you look through the output.

As you can see, you'll need to find the UTI for the application you want to use.  The UTIs for Safar and TextMate are in my example above, but to generically find the UTI for an application:

$ cd /Applications/MyApp.app/Contents
$ less Info.plist
...
        &lt;key&gt;CFBundleIdentifier&lt;/key&gt;
        &lt;string&gt;com.apple.Safari&lt;/string&gt;
...


NOTE: I have no idea what constitutes the difference between LSHandlerRoleAll and LSHandlerRoleViewer.  I can't find documentation on that anywhere.  What I do see is that 99% of the time LSHandlerRoleAll is the only one set (i.e. there is no LSHandlerRoleViewer at all) and that it is set to the UTI for the application that you desire to associate the type with.

Having brought you this far, I'm going to leave HOW to set the values you want as an exercise for the reader.  Messing with these things can be somewhat dangerous.  It is entirely possible for you to screw up a file and not have ANY of your file associations work.  Then you have to throw away the file and start over.

Some hints:


Read up on defaults write and its syntax
Take a look at PlistBuddy.  man PlistBuddy and /usr/libexec/PlistBuddy -h
Skip all this nonsense altogether and use RCDefaultApp