Fun thing with symbolic linked stuff...I use them under Linux (Ubuntu 10.04 Server edition) and my file-manager of choice 'Midnight commander', but it is always tricky when you want to remove them. it is very easy to not only remove the link, but the file/folder as well.
However, I do like to use them for making stuff available (within limits) in a 'walled-off' folder structure. I don't lose any sleep over the access to or the loss of content on that PC at all at any given time.
NTFS has proven to be more problematic to me. Specifically the NTFS version in Windows 2008 R2. When accessing it a lot through network for an hour or so (SOAP calls to Oracle database server), NTFS just told me that it was not able to access the hard disk anymore. And with a lot, I really mean a lot, as I was trying to mimic the traffic a computer with 64 Itanium processors needs to process (on a quad-core i7).
I lost two 350 GByte databases that day, as Oracle couldn't make heads or tales anymore from the mess NTFS had created. Even the archive logs from Oracle were damaged. And the funny thing was that I had an older version of one of these databases running on a (AMD single core) 2003 Server and that one was able to complete my test without any problem for any amount of time while not really being slower at all.
Because of this incident I do not have the same confidence in the latest version(s) of NTFS as in the older NTFS version(s) from 2003/XP.
Back to the topic again. Directory opus ( and higher has functionality comparable with the Libraries in Windows and I already dislike it in DOpus, so don't expect me to use it in Windows 7/2008. Never worked with folder junctions, so no (good/bad) comment from me on that matter.
An intelligent (to me at least
) folder structure with symbolic links always made more sense to me. More fine-grained control, (likely) more speed gaining access to the accumulated data and (likely) faster updates from file changes. But that could all be just me.