Dak and Aldrea, without question. Dak probably would have been my favorite character in the series, except that he was only in one book.
For some reason, Dak and Aldrea's particular struggle really got to me. Much more so than a human and an Andalite or a human and a hawk, an Andalite and a Hork-Bajir are simply two species that were not meant to fall in love with one another. You've got a peaceful, stupid, innocent race on the one side, and a militaristic, highly intelligent, arrogant race on the other. Yet they still managed to overcome that. Throughout the book, you can see both Dak and Aldrea gradually growing towards the other. Dak becomes more intelligent and even a teeny bit ruthless, and Aldrea becomes more compassionate and willing to do what is right rather than just what is logical.
I think Tobias/Rachel is incredibly romantic, and Elfangor/Loren was heartbreaking, but Dak/Aldrea was so romantically heartbreaking that I couldn't really choose anything else.
I didn't really like Cassie/Jake all that much. Mostly because I didn't like Cassie, and as the team's leader, Jake gave in to Cassie's moral ultimatums far more often than he should have. It struck me particularly in #46, when Jake basically said (and I'm paraphrasing, here), "We'll do whatever it takes to win, no matter what we have to sacrifice. . . unless, of course, Cassie doesn't want to."
Ax/Estrid bugged me, too. Yeah, they started out all romantic at the beginning. But they weren't meant for each other. Estrid is your typical Andalite, with all the ruthlessness and cold logic that that entails. Ax, at that point, had already become far too 'human' to really have a shot at someone like that. So they couldn't have worked out together. I think their 'relationship' in so much as it was one, was pretty much all hormones.