The Settings
General settings:
Settings are mostly stored in the /data subdirectory. If you're looking for something specific, start there.
Built-in apps:
Built-in apps tend to keep their settings in /data/data/com.android.* and /data/data/com.google.android.*
For example:
Contacts: /data/data/com.android.contacts
Email accounts: /data/data/com.android.email
MMS: /data/data/com.android.mms
WiFi:
WiFi settings location depends on the manufacturer, but is generally predictable.
Samsung Galaxy Pocket, S2, S3: /data/misc/wifi/wpa_supplicant.conf
Samsung Tab: /data/wifi/bcm_supp.conf
HTC Desire: /data/misc/wifi/wpa_supplicant.conf
Dell Streak: /data/misc/wifi/wpa.conf
Oneplus 2, 3: /data/misc/wifi/networkHistory.txt
Keyboard configs:
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.
Misc:
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.