Okay, here I go.
Top ten MANGA (not anime- screw anime):
Naruto- It's fight scenes and it's creative use of science in those fight scenes never fail to keep me occupied. Biology, Environmental Science, Medical Science and Psychology and predominant in the series.
Alive! The final evolution- Very very dark tone with a smut of humor, yet intriguing in it's own right. A spark of humans who has evolved and developed supernatural powers after a change-reaction of suicides, a boy wages war against such creatures, yet with powers of his own.
Holyland- A very dark yet realistic story that explores different types of fighting, with real life concepts. You will find many interesting facts about fighting and human behavior, it's like learning with a story.
Psyren- Similar to that of Alive! but different, with it's own concepts of powers and fighting abilities. Not much to give after this.
Spiral-Suiri no Kizuna- Following a child prodigy who investigates crimes and solves them, this is a manga with unconventional plot-lines. The puzzles and cases will always leave you guessing, and so will the characters. Also recommended along with this, Detective Conan and Death Note.
AIR- The first and the last romance/drama manga that I read, it's very very touching, and a lot less cheesy than it's anime counter-part. It might make you cry, be warned, it's anything but light (despite first inpression).
Full Metal Alchlemist- It has similar elements to that of Naruto,