You can (Uni)extract the installer, and you'll find all you need in the '{app}' folder. When run, Autorun Organizer saves settings to the system registry at 'HKCU\Software\ChemTable Software\Autorun Organizer' and it creates a folder tree at '%USERPROFILE%\Local Settings\Application Data\ChemTable Software'; it also asks for permission to go online and retrieve application popularity rankings.
Running Dependency Walker it also possible to see that 'ChemtableStartupChecker.exe' and 'Updater.exe' aren't directly linked by the main executable, which also doesn't seem to deal very well with system variables (e.g., '%systemroot%'); moreover, 'ProgramDataStorage.const' is a text file with several program paths inside, but I haven't tried changing them.
Autorun Organizer does provide for an easy way to check various autorun locations from a common interface, so anyway I put together a basic yaP launcher config for Autorun Organizer at http://pastebin.com/bUidUc0y.
author of http://www.chemtable.com/autorun-organizer.htm wrote:Autorun Organizer [is an] advanced autorun manager for Windows: speeds up boot up and overall Windows performance; manages autorun priorities; turns on/off programs in autorun; automatically controls disabled programs; absolutely free.
Download Autorun Organizer latest installer (v1.25) from http://www.chemtable.com/autorun-organizer.htm.