For me, the original minicomics will always be the best and most meaningful MOTU comics. DC's original miniseries and the MVCreations series were both strong. Marvel's Star Comics imprint of MOTU comics was far more miss than hit, but the final two issues - #12 and #13 - were paragons of Masters sequential art:
One of, if not the best, MOTU comics was fanfiction, but done by Emiliano Santalucia who later went on to illustrate the official comic series, boxart, to unofficially help design toys and now works for Hasbro, believe it or not. He's the Don Figueroa of Masters fandom. He made 'Homecoming' as an art student, but it is amazing and can be read here:
http://www.mastersunbound.com/specia...ming_page1.htm
(It's set on Eternia after The New Adventures of He-Man.)