Ok, sometimes i store settings via a database, and sometimes i use flatfiles.
i think that storing them in a database is better, mainly because i think databases are better for that type of storage. they also cut down in files on your sever, and bandwith to load the settings file.
so when you code custom apps, how do u store ur settings?
I'm a pretty big MySQL database kinda person when it comes to programming in PHP and MySQL. I used to use flat-files, however I find that databases are much easier to implement (for me anyway) and are a lot easier to call up on the fly.
If there is relational data that is being stored (multiple tables/files that relate to other tables/files) then database.
If it's just a simple list of settings (something=something) then a flat file.
Each has it's place and it all depends what you want to do. It even depends on the technology as well. An embedded SQL database may take the place of a flat file and might be a better solution because it can be cached and all run from memory which eliminates expensive disk access. If you're a good enough programmer then a flat file system can be cached to memory as well and kept there for an entire session (security may be an issue). Again, it all depends.