My favourite couple is Lucy & Kouta from Elfen Lied. But I also like Kiba and Cheza from Wolf's Rain, Gohan & Videl from DBZ, Iason and Ricky from Ai no Kusabi... There are not many good anime couples I know...
syaoran and sakura from tsubasa chronicle
kaname and yuki from vampire knight
ranma and akane from ranma 1/2
otani and koizumi from lovely complex
sano or nakastu (i can't decide) and mizuki from hana kimi
shurei and ryuki from saiunkoku monogatari
sister rosette and chrono from chrono crusade