Portugrade and related tools will honor (even empty) file/var/db/pkg/insert_port_name/+IGNOREME. I found also some discussions in lists about portmaster and this file. However I don't know, on which level is this file searched/processed, especially if make commands in ports directories will take its existence in account. Some greping in global Makefiles for ports may give answer.
You may also define HOLD_PKGS in pkgtools.conf, but this is only portupgrade related, not system wide, as you asked.
Using globally defined KNOBS, as SirDice stated, or if clausule shown by jb_fvwm2 in /etc/make.conf[.local] are only system wide methods known to me.