I am using a powerful uninstaller called EasyClean (don't be cheated by it's name) to record every bit of modifications installation programs made to registry entries, harddisk's files and inis/any text files. Its website is
http://www.bkedv.de/easyclean.html.
It can export a more detailed but proprietary file regarding all or some of the changes.
Regarding automatic installation of programs using your method, I think you don't want your users to change installation settings which original installer would normally ask such as installation directory etc. But it's dangerous especially of registry part, for example:
1. some shared/system dlls are not copied to your harddisk and thus no need to register in your registry, either because your harddisk has a same or more recent copy of those dlls. But your client's system might not have those dlls, or they are older versions that need to be upgraded. So your hand-made installation zip will not install them properly and thus problems might occur in the future.
2. The uninstallation information recorded by original programs corresponding to installation on your particular system, so they might not be suitable for other systems which have different configurations.
3. Some shared dlls need to be registered by increasing index number in (most probably, for Windows9x systems) HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\Curr entVersion\SharedDLLs. The index number is used to tell programs' uninstallers whether those dlls can be removed when users uninstall them. So if your system have low index numbers for those newly installed dlls and you make the client's system's index numbers to the same, they may cause problems in uninstalling or upgrading in the future.
4. For some system files such as Visual Basic runtime files, OLE system files, or other files which are currently running in your client's pc, your hand-made exe will be normally not working as original installers because the latter will normally restart and install (or the other way) those system files before installing the applications. There is high risk if not properly installing system files for any application.
5. If your client's pc is running NT in restricted user mode, many registry entries and/or files that only admin can import or install ones, will most probably can't be installed by your hand-made installer.
Those are just some opinions popped out off my head, notthing special...except EasyClean(!)