Sounds like this scene, I could be wrong though.
http://www.mangago.me/read-manga/gentei_kareshi/mh/sa-c4.1/pg-5/
(╬ ̄皿 ̄)凸 OMG, HOW IN THE HELL ARE YOU SO GOOD AT IT!!!!!!!!!!! MY HEARTU IS LEAPING WITH JOY(I don't even know how you could figured it out when my description isn't even correct(probably because of your good memory(I bet you did amazing in physic(physic right?), anyway :) THANK YOU SO MUCH!!!!!ヾ(☆▽☆)
Well, I've been trying to find this manga and I search all over my tags for it(only 'school life', 'shounen ai', ' drama', and 'bittersweet' though), but I still couldn't find it. And I thought maybe there's someone in this site who might know so..This is how it star with:
a classroom in springtime with open window. The cherry blossom were booming and a petal fall to a desk to where a student was sitting alone. And another petal fall to a desk of another boy who is surrounded by friends(popular x unpopular). And the manga give us a full view of how that look....
And the mc was saying something about how their life was so different and I only remember that one scene and the other one thing I remember was the last chapter, it ends with something like maybe it was from the very beginning they were attracted to each other(because they were so different) or something like that.
But the only clue i could give you helpers is the beginning of how the manga goes. Sorry but please tell me if you even have a clue to what I'm saying, and if I find it first I'll comment it,
thank you