Site-level preferences are located in TWiki.TWikiPreferences, however this Main.TWikiPreferences prefs topic has override priority and should be used for local customisations. This allows for easier upgrades as you don't need to worry about the shipped preferences clobbering yours. It's easier to keep a handle on if you only copy over the settings you actually change.
Quick edit of existing preferences (edit the topic text to set new preferences)
FINALPREFERENCES locks site-level preferences that are not allowed to be overridden by WebPreferences or user preferences:
Image, URL and alternate tooltip text of the logo for this installation: you should change these settings for your site, or they can be overwridden in WebPreferences for individual webs by defining these variables there.
Broadcast message for skins supporting a %<nop>BROADCASTMESSAGE% at the top of the page: (IMPORTANT: Set to empty message if not used; #Comment out unused messages)
Set BROADCASTMESSAGE =
#Set BROADCASTMESSAGE = NOTE: Edit and Attach will be disabled today between 05:00 PM and 06:00 PM PDT (00:00 to 01:00 GMT) for a scheduled <nop>NMCO Wiki maintenance.
Users or groups allowed to create new top-level webs: (ex: WebCreatorsGroup? ). If set to nothing, only administrators will be able to do this.