"Please Save My Earth" is an absolute classic if you're into longer stories.
"Magic Knight Rayearth" by CLAMP is one of my all time favorites and only 6 volumes.
"Kenshin" (Samurai X) by Nobuhiro Watsuki takes place in Meiji Era of Japan and features a good story - although only in the first Arc.
From the newer ones I'd definitely recommend:
Skip Beat!
Detective Conan
One Piece
The Ancient Magus' Bride
....there are many more, hoewever these are my personal best ones =)