At the end of "Crisis on Infinite Earths", Superman Kal-L of Earth-2, his wife Lois Kent, Superboy-Prime and Alexander Luthor of Earth-3 all travelled to a "Paradise Dimension", and except for Kal-L's appearance in "The Kingdom" we've haven't seen them since.
Superboy-Prime's only other appearance was in "DC Comics Presents #87" and "Superman #414", which you probably already read beginning at:
http://superman.nu/tales2/comet/A contemporary take on Superboy-Prime was recently the subject of a four-part miniseries "Secret Identity". It was rather good, but I longed to see the original kid again after reading it. I posted some comments on Superboy-Prime in this forum at:
http://superman.nu/phpBB2/viewtopic.php?t=924