I've always been offended at the way the Serato developers just take the easy route of storing meta data directly in media files, but only just happened across a reason why I should make an angry internet post about it:

When reading music from a Read-Only source (like the HFS file system of Mac OS X whilst running Windows, or NTFS partition in OS X) I've noticed excessively bad buffer dropouts which are a result of trying to update file attributes.

Rather then catching an File Access Denied exception and moving on, the program just keeps trying to write to something that not even the system has access to.

To my mind it would seem a whole lot simpler to store the cue points, loops and gains etc into something like an XML or SQLite file, and is certainly something I would take preference to as I do not like my files being altered in the way iTunes and Scratch Live seem to.