There is no easy answer to your question, as there are probably implementations of each that are in use today. However, the older IP V4 is used more than the others. IPsec is used by many of the VPN devices currently being marketed. IP V6 will likely slowly become the standard, but it includes an IP V4 compatibility mode so that the transition from IP V4 can occur without having two disconnected Internets. At what point the Internet will become purely IP V6 is anyone's guess. The push for IP V6 will come mainly due to IP address space reasons (we're running out of IP numbers just like we're running out of area codes), not for security reasons.
As you noted, IP V4 does not have any inherent security features built in. You may want to refer to a question I answered on Feb. 26 regarding security loopholes in TCP/IP for more information.
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This was first published in March 2002