Truthfully, I did not care for Rin much, but after I finished all the routes, I realized that Rin is the sweetest, loneliest, purest female character I've ever encountered. I will re-play Katawa Shoujo to see Rin again.
Emi is second, I followed her good ending route the first time I played KS. Then comes Lilly and Hanako. Overall, KS is AWESOME, amazing story lines! I don't think anything else could ever top it... at least in a few years.