I believe the “Incompatible Software” directory was created by the system installer/updater (see
here). Sometimes, the installer sets aside software that you installed yourself that it knows won’t run on your system anymore. Incompatible software is usually also moved to /Library/SystemMigration.
As for the Install.X folder, this could be a temporary folder that was used during the installation. It is common that new files are written to a new temporary location and then moved over. May also have been a faulty app installer that wrote temporary files to the wrong path.
They are not present on clean systems. You can probably safely delete them if they haven’t been accessed since 2011. The old "User Guides And Information" alias seems to be broken too, probably obsolete by now.