We have the following:
iPhone native app, with login form that posts to:
A php script on remote web server which checks against MySQL user table.
For security, would it be best practice to use some two-way encryption to encrypt every request? including this initial login? otherwise the user and pass will simple be passed to the web app in the clear?
I suppose https would take care of it automatically...
Using https is probably the way to go. It's what it was designed for.
It would be very wise to use SSL or TLS (the protocols that HTTPS uses) to communicate with the server. You could likely get this set up rather easily on a *nix or Windows server using OpenSSL. If you're on a shared host, they likely have an option to purchase an SSL certificate that's valid for a given period of time. This is a fairly trivial process and usually requires about a week (average) with most hosts to get set up.
It should also be noted that while it is never a bad idea to encrypt the login process, it will not make your system more secure "over all" if you have a login from the web that is not secured. For instance, if you secure communication with mobile devices, but not with desktops or laptops, your security may be for nigh. The security of your application is only as strong as its weakest link, so securing your entire application (for all platforms) is very important.
Also, keep in mind that a user's login credentials are only as valuable as the data or resources that they protect: if you encrypt the login information, it is also a good idea to encrypt the rest of the application as well. Wireless sniffing technology could easily steal session data, private user information, or other sensitive data. Securing the entire user session--rather than just the login procedure--is in your users' best interest.
Hope this helps!