My two favorite couples are kind of random, but I like
Ranma/Akane from "Ranma 1/2"
The two just seem absolutely perfect for each other in every way. Even though "Ranma 1/2" is a comedy, you can really feel the affection between Ranma and Akane throughout the anime and manga, and their love grows in such a natural way that makes the relationship seem real despite being a fiction. The relationship goes back and forth a lot, but that just makes it seem even more genuine.
and
my favorite,
Shinichi/Ran from "Detective Conan"/"Case Closed"/"Meitantei Conan" (or whatever you wanna call it)
They're friends from childhood, and they both started loving each other as they got older, but they never confessed it. Then the crazy plot kicks in and pretty much does everything to tear Shinichi and Ran apart, but they continue to love each other throughout all of the terrible ordeals. Shinichi ends up spending every day with Ran without her even knowing he is there, and he cannot hold her in his arms or tell her how he feels. At the same time, Ran spends every day waiting for Shinichi and wondering if he will ever return to her. But on an almost daily basis, Shinichi risks his life to save Ran, and Ran continues to wait for Shinichi, no matter how much it hurts her to be away from him. The relationship between Shinichi and Ran is such an earnest and persistent love, that I can see no other fictional love taking its place as my favorite.