Pop quiz. You're building an application. What parameters do you put in your config file? The answer, like any other architectural question is, "It depends." On one extreme you spend a lot of time with your customers and bake everything into the application. Changing anything, from the name on the splash screen to the on-disk fully qualified path to the splash screen image is compiled right into the binary. On the other end, the only thing the application knows how to do is read a configuration file that tells it where to find the dynamic libraries and custom DSL files full of business logic that actually do anything.
Like any other tradeoff, the right answer lives somewhere between those two extremes, and is tightly coupled to your customer(s). As a rule of thumb, the bigger the spread of customers, whether it's scale (whatever that means), domain, expertise, commonality of use cases, etc, the more configurable you need to be. A simple single user personal checkbook application doesn't need much configuration. Some user info, some financial institute info, some categorization, and maybe a couple of other things. A US tax preparing application, on the other hand needs all that, plus a way to handle the different states and rules, including ones that change or get clarified after you ship.
So how do you approach the configuration challenge? First, think about your customer and what they need to do. What do they need to customize, and how often does it change? Can you come up with a sensible default for your majority case? Is there a convention you can follow for that default? Maybe the right answer is wizard that runs the first time (and maybe on demand) that walks the user through the setup. One nice thing about a wizard is that you can validate that the configuration chosen makes sense.
Another thing to think about is if the defaults are in the config file or the application. If it's in the file it's obvious what the knobs are at least, but then you get folks poking at them just to see what they do. And what if your customers don't make backups? They think they know what they want and change the default. How do they get it back? Maybe a better idea is a base configuration file they can't change with an override file. Safer, and probably easier to recover, but each level of override makes it that much harder to know what the actual configuration is.
But is a local configuration file the right place to store that information? In most cases, probably, but what about the enterprise? How do you centralize configuration? How do you keep things in sync? Central databases, Flagr, Puppet/Chef and pushed configuration? Semi-random user triggered pulls (`update-uber-home.sh` anyone)? All options, and unless you really understand the user problem you're trying to solve, you can't make the tradeoffs, let alone come up with the best answer.
When it comes time to figure out how to configure your configuration, it depends.