Why? Any 'good' web project in any other language also involves a framework, does it not? Ruby has Rails, Python has Django, etc.
It should be no surprise that structured and organized PHP is better than raw PHP, and that examples of well written PHP would probably involve a framework.
Although I suppose it could be argued that since PHP is intended for the web, it shouldn't need a framework, and it should support more of the features a framework provides out of the box than it does. Nevertheless, the pattern of a framework is as useful in PHP for the same reasons as it is elsewhere, so I don't believe it says anything negative about the language per se.
You're missing my point. I'm not the Op but had I been the one asking the question, I would love to see actual projects that have clean php code written (even if they were using a framework), rather than refer to how a framework itself is written.
Within the last year, I think, somebody posted a link on HN to early Facebook code. I hardly glanced at it, but I remember that it looked well-structured and perhaps well-commented.
Symfony is one of them and has some of the best PHP code out there:
https://github.com/symfony/symfony/
As well as Aura: https://github.com/auraphp
And Laravel: https://github.com/laravel/laravel