[jggimi]

When I have used ipsec.conf, I used automatic keying and automatic SAs. Here is an example, using FQDNs rather than IP addresses.

ike dynamic esp from egress to jggimi.jggimi.homeip.net \
    srcid netbook.jggimi.homeip.net dstid jggimi.jggimi.homeip.net

The key pairs are stored in different branches of the /etc/isakmpd/{private,pubkeys}/ structure. For FQDNs, as in this example, the public keys are stored in /etc/isakmpd/pubkeys/fqdn/ and the private key used locally is stored in /etc/isakmpd/private/. The public key filenames should be the FQDNs of the participating systems. I have always called the private key file local.key.

# ls -lR /etc/isakmpd/{pubkeys,private}
/etc/isakmpd/private:
total 4
-rw-------  1 root  wheel  1675 Dec 27    2009 local.key

/etc/isakmpd/pubkeys:
total 16
drwxr-xr-x  2 root  wheel  512 Feb  1 13:51 fqdn
drwxr-xr-x  2 root  wheel  512 Feb  1 13:51 ipv4
drwxr-xr-x  2 root  wheel  512 Feb  1 13:51 ipv6
drwxr-xr-x  2 root  wheel  512 Feb  1 13:51 ufqdn

/etc/isakmpd/pubkeys/fqdn:
total 8
-rw-r--r--  1 root  wheel  272 May  1  2010 jggimi.jggimi.homeip.net
-rw-r--r--  1 root  wheel  451 May  1  2010 netbook.jggimi.homeip.net

/etc/isakmpd/pubkeys/ipv4:

/etc/isakmpd/pubkeys/ipv6:

/etc/isakmpd/pubkeys/ufqdn:
#

Using IP addresses is similar, but the key files are stored in a different branch of the /etc/isakmpd tree. For IPv4 addresses, store the public keys in /etc/isakmpd/pubkeys/ipv4/, and their filenames should be their applicable ipv4 addresses.

EDITED TO ADD: This host key infrastructure is not the only possibility. This and other key management methods are documented in the isakmpd(8) man page, in the IKE Public Key Infrastructure section.