I define secondary characters as ones that aren't in the manga/anime always or almost always. Certainly primary protagonists, antoganists, love interests are ruled out. Characters that have some significance, maybe are a major player in a certain arc before falling to obscurity or a bit player throughout the entire work. With that in mind.
Mariko (Elfen Lied) - A classic example of how upbringing can influence a characters' psyche. Sadistic, some would say evil, yet incredibly vulnerable. Her story is heartbreaking, and gives rise to conflicting emotions from what she has been through to how cruel she can be.
Hiko Siejuro (Rurouni Kenshin) - The teacher of Himura Kenshin, and easily the most powerful character in the story. However maybe for that reason, he appears only rarely. A hermit who likes sake, is disgusted by human society, and lives by his own rules.
Sinkorhyo (Hoshin Engi) - He has one of the most unique visual designs (along with the spirit beast he rides) I've ever seen. Sort of a jester/clown influence. He can cause tons of powerful lightning to reign down, which is pretty cool. He is a loner who likes to watch, and helps whoever to make events more interesting rather than for any moral purpose.
Corkus (Berserk) - This is the type of guy you rarely find in manga/anime but is quite common in real life. He has a good heart but is jealous, whines and complains a lot, but talks big. His interactions with Guts, and Rickert are very entertaining.