I upgraded from v8 to v9 this morning, and all pre-existing Mathematica Notebook files (extension .nb) have been modified to open with the AppleScript editor.
This is easily remedied by applying the "Get Info" command on one of the notebooks; changing the "Open With:" item from "AppleScript Editor" to "Mathematica", and clicking the "Change All" button to effect the change for all notebook files --- but this has the nasty side effect of changing the modification date of all your notebook files to the current date&time!
This is unfortunate because notebooks in a given folder can no longer be compared by age.
I hope I made some error and this does not happen to others.....
If others wish to do this, you might wish to do this on a folder-by-folder basis: Select all the notebooks in a folder, press the option key along with the command key and you will get a single Get Info window for all your selected notebooks; this allows you to make the change for several notebooks at a time, but not all notebooks on your computer.
For those who have little or no use for the AppleScript editor, perhaps a different solution is to replace the AppleScript Editor application with an alias to the Mathematica application. I haven't tried this yet....
There may be utilities that allow you to change the "Open With" information without changing the file dates. I haven't searched for them yet.