I use the standard tool because i can delete anything safely. I did not realise you were talking about the Extended version.
I always delete setup files, they have done their job, (setting up a program) and are no longer needed. As for un-installing programs, they all come with their own un-installer so i cant see how it would relate to the setup files.
I think what the text is talking about is the Windows setup files. These are created when you install a Windows hot-fix or a security patch.
They store old files, so if you need to un-install a patch in the event of something going wrong you can, but if your system is running fine, and you don't think you will ever need to un-install the patch, then theres no need to keep them.
Setup logs on the other hand are entirely different, they are just that, logs, logs of what, and when, has been installed. If you need to know when a particular program was installed keep them, but they are safe to delete.
User/system error logs are just that too, logs.
They tend to be used by network administrators, although i know a few people who go through them just to keep an eye on what is going on in their system.
If you delete these, Vista will generate new ones if and when needed.
If there are no errors, you don't need problem Reporting and Solutions, and if you do there will be a new error log waiting.
Same goes with the Dump files, a new dump file will be generated as and when needed. If you have no errors then you don't need a dump log.
To wrap this up, all the logs and dumps are a history of what has been happening in you system. They are safe to remove, but if you do, you will be removing the history of your system, up to that point.
Of course, as soon as you delete them, Windows will start writing a new history.
Hope this helps a bit. Sorry it's so long.
Good luck.
Stuart.