I'd say most "big time" apps will be ready. Thinks like TweetBot, Facebook, Instagram. Any app that is basically a scrolling list with toolbars is incredibly easy to update.
For a properly built app with no "magic numbers" (hardcoded screen size values) it mainly requires a recompile with the new SDK.
But Apple did change some things in the iOS 6 SDK that could cause incompatibilities that may take longer to fix (The apps on the app store will work, just not the binaries the developer is working on.)
I updated my game Rocket Chimp and submitted last night, took only an hour or so. The main problem will be the app review queue, which is probably going to be jam packed. Hopefully they upped their review staff for the next month or so...
My guess is you will start to see 4" iPhone support updates coming in early next week. Of course a large majority will probably still be in review unfortunately.