Freenet is a distributed data store that users a lot of encryption to protect it's users, I don't think it could really be called a darknet.
.onion services reside inside the tor network and traffic destined for them never leaves the tor network, therefor never goes through any exit nodes.
I2P does not have exit nodes built into the system ,but some people do provide this service. Generally while most people use Tor to browser the internet with some anonymity, I2P users tend to have various services that run over I2P (such as file sharing).
Both Tor and I2P support hidden services(Tor), or eepsites(I2P) which are essentially websites which are hidden inside either the Tor or I2P network, if done correctly (not the easiest thing to do) it makes it very difficult to find the physical location of the server that the website is running from.
This is why TheSilkRoad is still able to operate despite being a fairly high profile target for the DOJ.
Which is more secure, Tor or I2P? I don't know, with regard to hidden services/eepsites they both work more or less in a similar manner, however I've not heard of any sites like SR on I2P, and therefor the I2P network has not been as tested as much (in terms of law enforcement trying to catch site operators).
Code wise, I2P is written in Java, Tor is written in C (I think), I don't think it makes much of a difference, both are already fairly mature systems.
Possibly the size of the network may also be taken into account, a larger network means more security if you're trying to hide in the crowd. If this is the case the Tor is more secure simply because more people use it.
You can have FREENET sites and its very secure. Is there any chance we could have TOR and I2P mirrors Nefario. It may attract more users due to them having better Anonymity and also means the GLBSE could still operate if the www version was attacked by hackers or governments.