Lovely Complex immediately comes to mind, then Kimi ni todoke, then denkgeki daisy, and then Beast Master. All shoujo manga
I really like Koukou Debut, in the first chapter you may think they have nothing in common, but then comes the others chapters and you see that they really care about each other and I just love a lot this manga.
Aoharaido is cool in the beggining, but then appear other girl (like many shoujo) and gets kinda sucks, because you can see the love between the main couple.
Oh! Also, one I'm reading right now is called Bambi to Dhole and it is amazing! But still ongoing so you would have to be patient and wait for updates...
Are there any good shoujo mangas out there in which the protagonists have really good compatibility? Like the kind of couple you see and think "They were made for each other." I don't usually read shoujo, but I'm interested just to take a peek.
Oh, if there are any yaoi/shonen ai mangas with the same premise... Don't hesitate to recommend.