At a technical level, S/MIME and PGP (or at least PGP/MIME) use cryptography essentially identically. Yet the two are treated as radically different models of email security because they diverge on the most important question of public key cryptography: how do you trust the identity of a public key? Trust is critical, as it is the only way to stop an active, man-in-the-middle (MITM) attack. MITM attacks are actually easier to pull off in email, since all email messages effectively have to pass through both the sender's and the recipients' email servers , allowing attackers to be able to pull off permanent, long-lasting MITM attacks .
S/MIME uses the same trust model that SSL uses, based on X.509 certificates and certificate authorities. X.509 certificates effectively work by providing a certificate that says who you are which is signed by another authority. In the original concept (as you might guess from the name "X.509"), the trusted authority was your telecom provider, and the certificates were furthermore intended to be a part of the global X.500 directory—a natural extension of the OSI internet model. The OSI model of the internet never gained traction, and the trusted telecom providers were replaced with trusted root CAs.
PGP, by contrast, uses a trust model that's generally known as the Web of Trust. Every user has a PGP key (containing their identity and their public key), and users can sign others' public keys. Trust generally flows from these signatures: if you trust a user, you know the keys that they sign are correct. The name "Web of Trust" comes from the vision that trust flows along the paths of signatures, building a tight web of trust.
And now for the controversial part of the post, the comparisons and critiques of these trust models. A disclaimer: I am not a security expert, although I am a programmer who revels in dreaming up arcane edge cases. I also don't use PGP at all, and use S/MIME to a very limited extent for some Mozilla work , although I did try a few abortive attempts to dogfood it in the past. I've attempted to replace personal experience with comprehensive research , but most existing critiques and comparisons of these two trust models are about 10-15 years old and predate several changes to CA certificate practices.
A basic tenet of development that I have found is that the average user is fairly ignorant. At the same time, a lot of the defense of trust models, both CAs and Web of Trust, tends to hinge on configurability. How many people, for example, know how to add or remove a CA root from Firefox, Windows, or Android? Even among the subgroup of Mozilla developers, I suspect the number of people who know how to do so are rather few. Or in the case of PGP, how many people know how to change the maximum path length? Or even understand the security implications of doing so?
Seen in the light of ignorant users, the Web of Trust is a UX disaster. Its entire security model is predicated on having users precisely specify how much they trust other people to trust others (ultimate, full, marginal, none, unknown) and also on having them continually do out-of-band verification procedures and publicly reporting those steps. In 1998, a seminal paper on the usability of a GUI for PGP encryption came to the conclusion that the UI was effectively unusable for users, to the point that only a third of the users were able to send an encrypted email (and even then, only with significant help from the test administrators), and a quarter managed to publicly announce their private keys at some point, which is pretty much the worst thing you can do. They also noted that the complex trust UI was never used by participants, although the failure of many users to get that far makes generalization dangerous . While newer versions of security UI have undoubtedly fixed many of the original issues found (in no small part due to the paper, one of the first to argue that usability is integral, not orthogonal, to security), I have yet to find an actual study on the usability of the trust model itself.
The Web of Trust has other faults. The notion of "marginal" trust it turns out is rather broken: if you marginally trust a user who has two keys who both signed another person's key, that's the same as fully trusting a user with one key who signed that key. There are several proposals for different trust formulas , but none of them have caught on in practice to my knowledge.
A hidden fault is associated with its manner of presentation: in sharp contrast to CAs, the Web of Trust appears to not delegate trust, but any practical widespread deployment needs to solve the problem of contacting people who have had no prior contact. Combined with the need to bootstrap new users, this implies that there needs to be some keys that have signed a lot of other keys that are essentially default-trusted—in other words, a CA, a fact sometimes lost on advocates of the Web of Trust.
That said, a valid point in favor of the Web of Trust is that it more easily allows people to distrust CAs if they wish to. While I'm skeptical of its utility to a broader audience, the ability to do so for is crucial for a not-insignificant portion of the population, and it's important enough to be explicitly called out.
X.509 certificates are most commonly discussed in the context of SSL/TLS connections, so I'll discuss them in that context as well, as the implications for S/MIME are mostly the same. Almost all criticism of this trust model essentially boils down to a single complaint: certificate authorities aren't trustworthy. A historical criticism is that the addition of CAs to the main root trust stores was ad-hoc. Since then, however, the main oligopoly of these root stores (Microsoft, Apple, Google, and Mozilla) have made their policies public and clear . The introduction of the CA/Browser Forum in 2005, with a collection of major CAs and the major browsers as members, and several  helps in articulating common policies. These policies, simplified immensely, boil down to:
- You must verify information (depending on certificate type). This information must be relatively recent.
- You must not use weak algorithms in your certificates (e.g., no MD5).
- You must not make certificates that are valid for too long.
- You must maintain revocation checking services.
- You must have fairly stringent physical and digital security practices and intrusion detection mechanisms.
- You must be [externally] audited every year that you follow the above rules.
- If you screw up, we can kick you out.
I'm not going to claim that this is necessarily the best policy or even that any policy can feasibly stop intrusions from happening. But it's a policy, so CAs must abide by some set of rules.
Another CA criticism is the fear that they may be suborned by national government spy agencies. I find this claim underwhelming, considering that the number of certificates acquired by intrusions that were used in the wild is larger than the number of certificates acquired by national governments that were used in the wild: 1 and 0, respectively. Yet no one complains about the untrustworthiness of CAs due to their ability to be hacked by outsiders. Another attack is that CAs are controlled by profit-seeking corporations, which misses the point because the business of CAs is not selling certificates but selling their access to the root databases. As we will see shortly, jeopardizing that access is a great way for a CA to go out of business.
To understand issues involving CAs in greater detail, there are two CAs that are particularly useful to look at. The first is CACert. CACert is favored by many by its attempt to handle X.509 certificates in a Web of Trust model, so invariably every public discussion about CACert ends up devolving into an attack on other CAs for their perceived capture by national governments or corporate interests. Yet what many of the proponents for inclusion of CACert miss (or dismiss) is the fact that CACert actually failed the required audit, and it is unlikely to ever pass an audit. This shows a central failure of both CAs and Web of Trust: different people have different definitions of "trust," and in the case of CACert, some people are favoring a subjective definition (I trust their owners because they're not evil) when an objective definition fails (in this case, that the root signing key is securely kept).
The other CA of note here is DigiNotar. In July 2011, some hackers managed to acquire a few fraudulent certificates by hacking into DigiNotar's systems. By late August, people had become aware of these certificates being used in practice  to intercept communications, mostly in Iran. The use appears to have been caught after Chromium updates failed due to invalid certificate fingerprints. After it became clear that the fraudulent certificates were not limited to a single fake Google certificate, and that DigiNotar had failed to notify potentially affected companies of its breach, DigiNotar was swiftly removed from all of the trust databases. It ended up declaring bankruptcy within two weeks.
DigiNotar indicates several things. One, SSL MITM attacks are not theoretical (I have seen at least two or three security experts advising pre-DigiNotar that SSL MITM attacks are "theoretical" and therefore the wrong target for security mechanisms). Two, keeping the trust of browsers is necessary for commercial operation of CAs. Three, the notion that a CA is "too big to fail" is false: DigiNotar played an important role in the Dutch community as a major CA and the operator of Staat der Nederlanden. Yet when DigiNotar screwed up and lost its trust, it was swiftly kicked out despite this role. I suspect that even Verisign could be kicked out if it manages to screw up badly enough.
This isn't to say that the CA model isn't problematic. But the source of its problems is that delegating trust isn't a feasible model in the first place, a problem that it shares with the Web of Trust as well. Different notions of what "trust" actually means and the uncertainty that gets introduced as chains of trust get longer both make delegating trust weak to both social engineering and technical engineering attacks. There appears to be an increasing consensus that the best way forward is some variant of key pinning, much akin to how SSH works: once you know someone's public key, you complain if that public key appears to change, even if it appears to be "trusted." This does leave people open to attacks on first use, and the question of what to do when you need to legitimately re-key is not easy to solve.
In short, both CAs and the Web of Trust have issues. Whether or not you should prefer S/MIME or PGP ultimately comes down to the very conscious question of how you want to deal with trust—a question without a clear, obvious answer. If I appear to be painting CAs and S/MIME in a positive light and the Web of Trust and PGP in a negative one in this post, it is more because I am trying to focus on the positions less commonly taken to balance perspective on the internet. In my next post, I'll round out the discussion on email security by explaining why email security has seen poor uptake and answering the question as to which email security protocol is most popular. The answer may surprise you!
 Strictly speaking, you can bypass the sender's SMTP server. In practice, this is considered a hole in the SMTP system that email providers are trying to plug.
 I've had 13 different connections to the internet in the same time as I've had my main email address, not counting all the public wifis that I have used. Whereas an attacker would find it extraordinarily difficult to intercept all of my SSH sessions for a MITM attack, intercepting all of my email sessions is clearly far easier if the attacker were my email provider.
 Before you read too much into this personal choice of S/MIME over PGP, it's entirely motivated by a simple concern: S/MIME is built into Thunderbird; PGP is not. As someone who does a lot of Thunderbird development work that could easily break the Enigmail extension locally, needing to use an extension would be disruptive to workflow.
 This is not to say that I don't heavily research many of my other posts, but I did go so far for this one as to actually start going through a lot of published journals in an attempt to find information.
 It's questionable how well the usability of a trust model UI can be measured in a lab setting, since the observer effect is particularly strong for all metrics of trust.
 The web of trust makes a nice graph, and graphs invite lots of interesting mathematical metrics. I've always been partial to eigenvectors of the graph, myself.
 Mozilla's policy for addition to NSS is basically the standard policy adopted by all open-source Linux or BSD distributions, seeing as OpenSSL never attempted to produce a root database.
 It looks to me that it's the browsers who are more in charge in this forum than the CAs.
 To my knowledge, this is the first—and so far only—attempt to actively MITM an SSL connection.