Just ran into a Development Infrastructure for PHP which discusses a generalized strategy which Tony uses when building applications with PHP. He clarifys some of the design decisions further in the FAQ.

Think Tony's done an excellent job - it's an end to end view of the approach he's evolved for building web applications and is also more or less a first - I've yet to see anyone be bold enough to describe a complete PHP architecture in this kind of detail.

I actually listed this same resource in an upcoming PHP Magazine concerning the frameworks (specifically MVC), and it is quite good - especially if you're looking for an easy to use. Harry talks about it a bit more - There's alot of valuable insight in there and get the general impression of "sanity" (i.e. taking into account PHP's inherent advantages and disadvantages).