As it turns out, there is no magic file or directory that contains all settings. They are stored in various places, and depends greatly on how the manufacturer decides to set things up. I primarily work with Samsung phones, so the information here will mostly be Samsung oriented. Also, note that all of the below requires root access. If anyone has anything to add / rectify, feel free to comment.
First off, I have found that "copying settings" is not always the best way to go. You can do nandroid backups and restores, which pretty much clones one phone to another. If you're technical enough, and you're using Samsung, then creating your own odin image might be an even better option as it doesn't rely on you or someone else having created nandroid / recovery support.
Settings are mostly stored in the
/data subdirectory. If you're looking for something specific, start there.
Built-in apps tend to keep their settings in
WiFi settings location depends on the manufacturer, but is generally predictable.
Samsung Galaxy Pocket, S2, S3:
I have had to disable hardware keys, reconfigure layouts, or alter general keyboard behaviour before. The exact file name tends to be different on every phone, but I've found the config files to always be in
/system/usr/keylayout/. Be careful, as breaking those could render your phone unusable.
Most miscellaneous settings like product information, boot sounds, and enabling / disabling the on-screen nav bar are stored in
/system/build.prop. Breaking this config file could bootloop your device.
If I find more information, I'll add later.