Understanding this stuff REALLY works is actually pretty hard - it does need a dark room and an ice-pack.
It is complicated by the fact that different OSes (Windows/Linux/Unix) and different file systems (NTFS, ext2/3, Reiser etc.) use similar terms to refer to somewhat different things and work differently internally.
I think that I've got it figured out, thanks to an excellent article at
http://shell-shocked.org/article.php?id=284
I'm writing a condensed summary for myself in order to make quite sure that it's all clear in my head - if anyone is interested I'll post it here.