For OpenSMTPD users, smtpd.conf syntax changed (ssl, certificate, from, helo), see the upgrade faq and the smtpd.conf man page. (Should be easy, though)
The venerable popa3d POP3 deamon has been removed from the base system. You will need to replace it with something else. An openports.se search for packages matching "pop3" in their descriptions turn up quite a few candidates.
The identd identification protocol daemon has been rewritten and is no longer called by the inetd 'super server'. sysmerge will usually remove the relevant /etc/inetd.conf entries; if you want to run the service, you need to edit your /etc/rc.conf.local to include a identd_flags= line with relevant flags (usually just "-e".
On i386, java is no longer available as a package. If you need to run Java code, you need to upgrade to AMD64 if your hardware is compatible with that platform. Sorry, no Java on your Soekris. And tough luck, Oracle doesn't care either.