What are the differences between OpenSwan and StrongSwan? All I found is this comparison between the outdated FreeSwan and testing version of OpenSwan - i.e. current stable of OpenSwan is 2.6 (3.0 in comparison) and current stable for StrongSwan is 4.4 (4.1.7 in comparison) which seems grossly unfair (there is no point in comparing Windows 98 with Ubuntu 10.10 or Mac OS X 10.7 with Slackware 8.0).
After reading some websites, StrongSwan seems to be better maintained while OpenSwan seems to be more popular.
Libreswan is the project the Openswan developers created after the company they had originally founded to develop Openswan sued them over the trademark. So Libreswan is what we will discuss here.
The most obvious differences are:
Distro support:
IPSec-tools was a port of the KAME IPSec userland from BSD to Linux. It appears to be no longer maintained.
NOTE: See the other answer, this one was correct in 2011, but the landscape has changed in that time and this is no longer the correct answer to the OP's question.
Both OpenSwan and StrongSwan are forks for continued development after FreeS/WAN project closed up shop. However, most of the Linux distributions have moved more towards IPsec-Tools since then.
You can use either one for IPsec on Linux, but unless you have a specific need for them, or you are trying to maintain configuration compatibility with older FreeS/WAN setups, you are probably better off using IPsec-Tools and Racoon (ISAKMP daemon from IPsec-Tools) for any new Linux IPSec Setups.