Are external configuration files considered an antipattern?

Question

Many times I have been in a situation where an application is apparently broken, only to find that an external configuration file has been at fault. Typically this is because the wrong file is there, or that it contains incorrect data.

Is there a better way to allow an external user/process to modify the runtime characteristics of an application, or is this the best known solution to the problem?

I'd like to see discussion on the general case rather than focusing on, say, Unix /etc or Java JNDI and so on.