Junjou Romantica is probably the most famous one. I really like the anime, but haven't read the manga. Papa to kiss in the Dark is quite good, only seen the anime again. Has incest and stuff, but if you don't mind that
I haven't actually watched that many animes, mostly just read mangas. But if you like school stories, Our Everlasting has got to be my favorite one ever. You Will Fall in Love is also kind of school-life. Also Menkui (Suzuki Tanaka), and June Pride (Shinobu Gotoh/Kazumi Ohya) are school settings.
Desire, that's a pretty famous school type manga as well