Mmm... for web dev I like URL based file organisation to a degree... It depends alot on the system that's in use though; some systems work better if you organise your application code around the locations where a user is likely to use it, and in a way that's a background intention to PHP; "I can put a program anywhere on my server!". Although; personally, I don't think PHP itself brings many new principles to ANY kind of development.
What I personally dislike; is the seemingly magical index.php; which spits out different content based on a 'page' query string - I like folder division and file-naming based about functionality; in the same way as I would when working with Word documents offline; I like to see 'descriptive URLS' that indicate the web developer has a modular, flexible, and most importantly content-centric site... Otherwise; if it just feels like a site, that is clearly organised around one central, versioned 'application', that feels like it isn't going to be a constant source of useful information. And hey.. don't use URL rewrites to mask out your index.php?page=home.. I'll see right through it ^_-
That applies with or without server-side code; HTML pages have an inner hierachal structure; it makes a helluva lot of sense for that hierachy to spill up into the filesystem aswell..
Program code organisation; I need some levels in there; it pertains to easier updates; plugins; automatic compilation rules; even runtime 'special effects' if it's an interpretted language.
I'd say a good folder hierachy is possibly the most important thing to me if I'm going through someone else's code... It's easier to know where to start looking for something by looking in the obviously named folder; than by following a trail of includes/imports/codepulls/magipeeks.
But, that means intelligent division of code into files has to go on somewhere. PHP among other interpretted languages doesn't always pertain to good division of code into 'class files', or even into classes atall... Still even C(++) has that problem.
Java's gotta win outright for 'forcing' division of code into files; and even division of code into folders if one wants to use hierachal packaging within code.. I'm sure they nicked/borrowed that idea from somewhere though; but I'm not old enough to have experience of such things =P