An IRC friend of mine is a big proponent of I2P and wants everyone to use it, and it does let you do some cool things, like bittorrent and human-readable pseudo-domains, but ultimately the reason I can't bring myself to use I2P and Freenet is because I can't get over the fact that my IP address is exposed to random nodes on the network. I like the privacy that entry guards afford.
I have never been very impressed by I2P, although it does seem to have the most vocal group of proponents. I personally see it as being similar to the Apple of anonymity networks, it has a hardcore fan base of people who know it is the best, but they don't seem to quite know why it is the best. I guess I would compare Tor to Linux and Freenet to BSD.
The fact that it is so easy to enumerate the IP addresses of everybody who uses I2P is also one of the reasons why I will not even touch it. Freenet is not so weak to this because of Darknet mode, which can be used after running in Open Net mode to essentially give yourself at least the same membership concealment provided by Tor entry guards.
I also trust the relays more. There's a big, publicly accessible list of all the relays, with lots of info about them: hostname, geolocation, bandwidth, (usually real) contact info. You can see them running for months at a time, and people run scripts against them regularly to determine if they are acting maliciously. It makes me feel safer than connecting to some random, unknown IP address.
People run scripts against them to see if they are acting maliciously, but that only applies to exit nodes. Freenet has no exit nodes so there is no need (or even ability really) to run scripts against them trying to see if they are malicious or not.
There's also the fact that I2P and Freenet are so small. On Tor, you're one of 500K daily users. That's a nice, big crowd to mix in with, compared to I2P's 20K simultaneous users. I don't know how many users Freenet has, but presumably it's even fewer.
Freenet is also estimated to have about 20K simultaneous users. There are two ways of looking at this though. Tor certainly has the most concurrent users, I think it actually serves over a million people per day now. On the other hand, Tor has the least routing nodes of the three major anonymity networks (Tor, I2P, Freenet). Tor has about 3,500 routing nodes, I2P and Freenet have about 20,000 routing nodes each. You get anonymity gains by having a bigger userbase as well as by having more routing nodes (in the case of I2P and Freenet clients and routing nodes have about a 1:1 ratio, for Tor the ratio has been about 400:1 .) If somebody can see Tor exit traffic, they know the traffic originated from one out of over a million possible Tor users (since more than a million people use Tor, just not at the same time). On the other hand, if they see content published to Freenet, or somebody accessing an Eepsite, that content/access came from one out of only about 20,000 users. Looking at it another way, assuming all nodes route the same amount of traffic (which they certainly do not, but for the sake of argument. In reality we would need to compare bandwidth added). an attacker who adds 1,750 nodes to Tor can see roughly 50% of the traffic routed through Tor, an attacker who adds 1,750 nodes to I2P can only see 8.75% of traffic routed. In the case of Freenet this isn't comparable though because Freenet works very differently from Tor and I2P.
So from the start your anonymity with Tor is greater than your anonymity with I2P or Freenet, because you have a much larger set size to blend into. But from the specific perspective of an end point timing attack (by far the most worrying attack against Tor), you will be anonymous to the set size until you are deanonymized. This is really roughly speaking though because there are so many other things to take into consideration, but for the most part I think many users of Tor (especially the non-pseudonymous ones) will continue to be anonymous to the set size of users until they are deanonymized with a timing attack. Having a bigger set size to blend into at first is beneficial, but the risk of falling victim to a totally deanonymizing timing attack is also a lot higher because the number of routing nodes is a lot smaller (and therefor it is easier for an attacker to control a larger percentage of them).
The size and diversity of the Tor crowd are big privacy-protecting features. If you run a Freenet node, there's like an 80% that you're a pedophile, but if you connect to Tor, there' s maybe a 10% chance you buy drugs, a 10% chance you're a pedo, a 5% chance you're a journalist, or whistle blower, or intelligence agent, or political dissident, or just somebody who is privacy conscious, or paranoid, or curious. There are way too many groups to conclude anything about a Tor user, if you can only watch their end.
Yes I agree entirely, Tor having so many users is a huge advantage for it. However, I2P having so many routing nodes is also an advantage for it. There is a huge chance somebody using Freenet for a prolonged period of time is involved in CP, however actually proving that is very difficult.
Overall I definitely like Tor the most. It also has the enormous benefit of allowing traffic to exit the network. I2P is weak to an assortment of attacks that Tor is well protected from (although I2P is better protected against other attacks that Tor is not well protected from, for example internal timing attacks), Freenet is difficult to use for service providers, etc.