According to Conservapedia, "Pharyngula is known for its sarcastic and often specious criticism of creation science and intelligent design theory, as well as regular postings of photos of cephalopods (often with vulgar sexual connotations both subtle and blatant)."  PZ is, however, careful to cancel out the risk of cephalosexual corruption by the occasional posting of photographs of himself, which are alleged in the present sentence to be at least three times as effective for the purpose as a cold shower.
It is from the pharyngula stage of vertebrate embryonic development, where the embryo has a notochord, a spinal cord, a tail, and gill grooves and pouches at the pharynx or throat. That inspiration was likely from PZ's research on zebrafish, with their readily-accessible embryonic stages of development.
Topics taken up on Pharyngula include
- Theist excesses
- restriction of liberties in the name of religion
- imposing religion in public (especially in education)
- some examples of exceptional theist stupidity
- Atheism and Theism
- science denial: Global warming denial, anti-vaxxers
- alternative medicine
- New Age beliefs
- Political issues. As the tagline is "evolution, development, and random biological ejaculations from a godless liberal", there is regular criticism of:
- social injustice and inequality
- Internet censorship Pharyngula shut down for a day during the protest against SOPA and PIPA.
Some notable posts
- The Dear Emma B letter, June 23, 2011, which has been nominated for The Open Laboratory 2011 
- The Courtier's Reply, December 24, 2006 
- Crackergate, July 24, 2009 
- Deep Rifts, November 9, 2009 
- Myers' Law, April 19, 2008 
- Visiting the Creation "Museum" , August 10, 2009 
A popular feature of the blog is the Endless Thread, a repository for all manner of on- and off-topic topics (often with vulgar sexual connotations both subtle and blatant). The Endless Thread has been going since February 2009.
Other serial features include
- I get email
- Why I am an atheist, started on October 10, 2011.
- Mary's Monday Metazoan
- Botanical Wednesday
- The Friday cephalopod
- Sunday Sacrilege (as of October 2011, there have been no new posts in this category for a year)
There may be changes in the way Pharyngula comments are managed.  PZ feels Thunderdome is in meltdown and is sorry Chris Clarke left. PZ wants the horde to suggest ways of getting the "knifey-bitey-smashy atmosphere to lighten up a little. Just a little." 
There are two pages accessible from the tabs for two specific groups:
- The Order of the Molly for distinguished commenters
- The Dungeon for banned trolls
A blog such as Pharyngula also participates in many internet memes, for instance Poe's Law and SIWOTI syndrome figure prominently among them (see this category page for more). There is also a list of the internet memes exclusive to Pharyngula (or in some other cases, to other science and atheism blogs). Also there are a number of abbreviations that might be opaque to newcomers.
The blog attracts a lot of trolls, the majority of whom do not get banned and thus do not end up in the dungeon.
There have been waves of trolls on Pharyngula associated with certain groups or websites:
- You're Not Helping, a massive case of sockpuppetry as revealed in June 2010
- The Slimepit has become a new home to many antifeminist trolls after Elevator Gate in June 2011
But the vast majority of trolls appear to be unaffiliated. They can be documented in the Troll Watch list.
- Blockquote failure
- Pre-2006 archives
Adapted from Pharyngula Wiki