I have a Web site configured to run in a custom application pool. The pool identify is set to a domain user.
I can change the users password using IIS Manager, but is there a command line method ?
You can use the ADSUTIL.VBS tool to do this from the commandline (or steal the code from it for your own custom script).
The properties that you are interested in are all documented on MSDN at Metabase Properties.
The following is an example of how to create a new Application Pool called "MyAppPool" and configure it to use a custom Application Pool identity of domain\username with a password of pass. You can find all the property syntax and valid values in the MSDN. Remember, if you want to use the space character as a parameter, you have to put it in double-quotes since the commandline processor uses space as parameter delimiter.
CSCRIPT %SYSTEMDRIVE%\Inetpub\AdminScripts\ADSUTIL.VBS CREATE w3svc/AppPools/MyAppPool IIsApplicationPool
CSCRIPT %SYSTEMDRIVE%\Inetpub\AdminScripts\ADSUTIL.VBS SET w3svc/AppPools/MyAppPool/WamUserName "domain\username"
CSCRIPT %SYSTEMDRIVE%\Inetpub\AdminScripts\ADSUTIL.VBS SET w3svc/AppPools/MyAppPool/WamUserPass "pass"
CSCRIPT %SYSTEMDRIVE%\Inetpub\AdminScripts\ADSUTIL.VBS SET w3svc/AppPools/MyAppPool/AppPoolIdentityType 3