Kareshi Kanojo no Jijou (His and Her Circumstances) or Karekano for short.
I'll say Karekano is high up even among my favorites. It's a shoujo manga that ran from '96 to 2005. I read all of it this year and it's amazing.
While a lot of shoujo stories depend on misunderstandings and other dull things to dramatize things, Karekano uses inner conflict awesomely and it has one of the greatest buildups and endings I've seen in romance stories so far. And the comedy is really funny too. Going beyond the main couple getting together, it becomes a genuine story about finding oneself. From the journey to the conclusion, it resonated with me greatly.
I'd recommend this, hands down.