I did not have to think about this for a long time: my favourite anime couple is definitely Jinta and Menma from Ano Hana. They are so adorable together! Even when they were still children they got along very well, and already then they were attracted to each other. These two characters are simply perfect together.
I love how they are so different yet the same. Menma is outgoing and cheerful, while Jinta is more of a shy person that does not speak a lot. Despite these differences they belong together, and they both realize that. Jinta is willing to give up a lot for his relationship with Menma, and Menma sees Jinta as “someone she wants to marry”. Jinta gets often annoyed by her childishness, but he truly loves her.