It's funny, because on the surface it seemed like an easy question to answer, but now that I think about it, I'm kind of conflicted. I liked all of the girls - even if I could never have a relationship with Shizune or Rin, I still ended up caring about them and considering them friends. If it's solely about which girl I liked the most, I've got my little banners in my sig. But then I had to consider which I felt was the best story overall, and I thought they were all good (even if Shizune's path bored me to tears at points). So ultimately I think I had to decide based on how much I could relate to Hisao's personality in each path.
My first path - where I answered based solely on what I would have done were I Hisao - had me pursuing Emi, which surprised me because I didn't really think of her as my type; while I'm attracted to outgoing, athletic girls, I've never been much for blondes or petite girls. I had been kind of following Hanako up until then. Hisao also struck me as a really boring person in this route; he never seemed to have anything to occupy himself with when he was alone, and that's something I've never had a problem with. But I stuck with it and found that it really resonated with me; the way Emi and Hisao teased each other and just got along in general, and the way in which she was always working to help him felt very much like some of my own romantic experiences (Emi also had a lot of traits in common with the girl I never got over, too, which I'm certain helped). The thing with her dad seemed really obvious to me from the start, so I spent some time shaking my head at Hisao's cluelessness, but I must admit that I have been equally clueless in the past, so there you go. Thus, my kneejerk reaction to the question would be to say it was Emi, and I'm not certain that would be an incorrect answer for me.
However, Hanako was the kind of girl I would have secretly had feelings for when I was in high school, and the way Hisao behaved in that path would very much have been like how I would have at least wanted to behave then. Hanako and I are both introverts who enjoy reading and games, so we'd certainly have a lot in common, too. While, like many others here, I would have liked to see more of their actual relationship, I thought that her Good Ending was quite poignant, and even the chapter title, "Adulthood", said quite a bit. She and Hisao were, for the first time, entering a mature relationship with each other, and would continue to open up as they got to know each other and shed the insecurities that had held them both back for so long. I even felt the change in Hisao as I was reading that final part (through my manly tears, of course) - it finally felt like he was just being himself with her, instead of talking through his "double-padded silk gloves" demeanor.
I thoroughly enjoyed Lilly's path, but that was the point at which I started to realize that each girl was probably going to require Hisao to have a mindset that was at least somewhat alien to me. Hisao in that path was so responsible and mature in the way he carried himself, and I know I've never been that confident, either in high school or now. Shizune's path was utterly foreign to me, and I fear I lost all emotional attachment to it half-way through. Only Misha's revelation tugged at my heartstrings, but then it was back to the personality types that I simply couldn't relate to. I'm glad that some of you can and did, though.
Rin is a special case. I could completely relate to Hisao's personality in her route, because I've been there, too. I've been the moody artistic type, and in my more depressed phases I behaved a lot like him. I did really poorly in high school not because I couldn't do the work, but because I just didn't feel like it and I preferred to draw or write roleplaying game stuff, and much later on, I attended art school. So it wasn't at all a huge stretch for me to get into his mindset in Rin's path. However, it was also depressing, because it reminded me so much of the parts of me I don't like (perhaps also appropriate). Rin's story spoke to me on a couple of levels, and while there were parts where I wasn't quite agreeing with the philosophical bits, for the most part it was a situation I could see myself experiencing. But it HURT so much, from start to finish. It was really a different kind of experience than the other routes had been; it was clearly a love story, but it was utterly unlike anything I've ever experienced.
In the end, I have to compliment the writers on all of the routes, because they were all so well-done.
tl;dr: A tie between Emi and Hanako.