My current iPhone app does exactly what you are describing. It consists of library on the iPhone called Objective Resource http://iphoneonrails.com/ which coverts the NSObject representation of for example a User object into JSON and communicates via HTTP over the 'net to a Ruby On Rails server http://rubyonrails.org/ which then runs queries against MySQL database which is basically like a free version of SQL Server. It's what you would call a three tier system http://en.wikipedia.org/wiki/Multitier_architecture: the iPhone client, the Ruby On Rails data access layer and MySQL database which is the database layer. This is pretty standard.
So what happens when the user types in his name and password in my system is that the iPhone app changes the name and password on User object. The Objective Resource library then translates the data contained in the User object into JSON and then posts it to my Ruby On Rails site. A method on one of controllers on the Ruby On Rails stack grabs the data then runs an Update on the Users table on the MySQL database.
You can run a variety of different data access layers such as PHP and ASP.NET and databases such as Postgres, SQL Server and Oracle. But Ruby On Rails is free and so is MySQL wheras some of the others aren't.