Where are "temporary files" cleaned by Windows 7 Disk Cleanup?

The "Temporary Files" folder that Disk Cleanup is referring to is the one pointed to by the environment variable %TEMP%. You can go directly to this folder by typing %TEMP% in the Run box or in the address bar in Windows Explorer.

Disk Cleanup's list of "places to cleanup" is stored in the registry key HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\VolumeCaches. The Temporary Files item is in a key named, unsurprisingly, Temporary Files.

I couldn't find anything other than %TEMP% in the registry key mentioned by Patrick, so I tried to log cleanmgr.exe using Process Monitor.

cleanmgr.exe does a File System Class SetDispositionInformationFile Operation with Delete: True Detail on files in %TEMP%, which in my case according to echo is equal to %LOCALAPPDATA%\Temp

It had already deleted the 3 GB unaccounted for by %TEMP% though, and didn't trim the 500+ MB C:\Windows\Logs\CBS\CBS.log; I suspect most of my wasted space was in winsxs.