Kaname. I know she loves both of them but in different ways, what I mean is, Yuuki loves Zero but it's a different love towards what she feels for Kaname. We can love our family, our friends, our animals or even the world around us, to yuuki Zero is a special and precious friend who yuki needs to protect and care. With Kaname is totally different SHE IS IN LOVE WITH HIM, She can't live without him, she wants him by her side forever, and SPOILER ALERT In the end of the manga with the extra chapters we can see that Yuuki is still waiting for Kaname while she is with Zero. Also (SPOILER) She waited hundred years to sacrifice her own life to make him human and live a normal life. I don't know what you think but I call it True and Epic Love!

The real answer is both of them.

^As I understood it, she waited til Zero had died before sacrificing herself to turn Kaname human. That seems more like she didn't want to keep living with Zero dead, as well as wanting to give Kaname the opportunity he'd previously wanted to give her.