Love Stage!!
Hitorijime My Hero
Betrayal Knows My Name
Ling Qi
Super Lovers
Those are some good ones that I don't hear people talk about that often.
I've also heard good things about the Kono Danshi series, but haven't watched it myself.
My personal favorite is a movie called Doukyuusei (Classmates) (pictured below). It's a really sweet, pure movie with a unique art style, and it's by far the best shounen-ai I've ever seen.
There's also No.6, which isn't a shounen-ai, but the main characters (both boys) are in a relationship, and their relationship is one of the best portrayed in anime in my opinion.