Here are a few examples of what I like about his content: he's dismantled creationist misinterpretations of science, pointed out serious flaws in a study on the efficacy of prayer, repeatedly shown that Hitler was not motivated by evolution or atheism (as many Christians claim), and become infamous to Catholics for deriding their doctrine of transubstantiation. While this rant about the absurdity of a young earth would probably be handwaved as "presumptuous" by YECs, I enjoy it because it showcases just how much evidence they have to ignore to maintain their beliefs. He's made a lot of great posts, but if I had to point to one example of his best work, it would be this devastating refutation of creationist Jonathan Wells' claims about Haeckel's embryos in the book Icons of Evolution.
I do tend to disagree with PZ somewhat when it comes to politics (he's a staunch liberal, while I'm more of a moderate). And while I disagree with accomodationists who think that science and religion should be best buddies, I also find his approach to creationism and theism a little too aggressive. He's fond of mockery and thinks it can be a powerful tool for dislodging people from their status quo beliefs. That's true to an extent, but I think sometimes he goes overboard and makes people more likely to become entrenched in their beliefs and demonize outsiders without considering what they have to say.
Overall, while I somewhat dislike PZ's brashness and some of his political views, I appreciate Pharyngula for its humor, informativeness, and frequent updates on current events.