I saw early postings about RunOnceEx in this mailing list circa January 2003, however the problems they presented were never fixed.
Some programs come with simple INF installers because people can cheaply create an INF file, and use a free Setup.exe bootstrap file that reads the name of an INF file from Setup.ini or something similar. These programs do not have any way of processing RunOnceEx themselves.
In the distant past before I had converted to Linux and wine, I used to deal with such programs quite a bit;
RunOnceEx was Microsoft's way of allowing simple installers to register files, especially if a reboot and wininit was necessary to overwrite files.
The basic structure of the registry format is: [Software\Microsoft\Windows\CurrentVersion\RunOnceEx\Number] "Number"="program.exe arguments" "Number"="c:\somepath\somedll.dll|SomeExportedFunction"
Number is nothing more than a number. All commands are processed in sequential order, first by key, then by value. If there is no pipe symbol in the line ('|'), the data of the value is executed as a program, with all following tokens passed on as arguments. However, if the pipe symbol is included, the portion to the left is treated as a DLL, and calls the exported function of the name to the right of the symbol.
Once all values in a key are processed, the key is deleted, and the process starts with the next key.
There is one subkey that has a special meaning: All keys/values in [Software\Microsoft\Windows\CurrentVersion\RunOnceEx\Setup] are not processed at boot-up. Rather, they are read by the program runonce.exe, not included in wine. It is through this key that one gets the annoying "Updating Windows" box in the upper left corner of the screen, listing tasks being performed. I believe Powertoys for Windows 98 utilized this feature, but I do not remember how.
However, these days RunOnceEx still has one important feature: Some people, like me, have programs that fail to load objects because the OS version is not set to XP. When the OS is set to xp, the install-ie6 script does not automatically process the RunOnceEx keys, failling to register all of the DLL's, including the Crypto support needed for programs such as Steam.
As such, for IE6 alone, users have to process 50+ lines by hand, in something that SHOULD be processed at bootup, via wineboot.