I gotta say, I highly prefer the visual novel, but who doesn't prefer the original material compared to adaptations. That aside, I highly enjoyed this anime. Definitely in my top 5 and every time I try recommending it to people, they enjoy it (except for one girl who doesn't like the art but then turns around and says she likes k-on despite not knowing that its the same anime studio).
I honestly think Tomoyo and Tomoya are best, especially since it's expanded much more in Tomoyo After and I just like Tomoyo much more than the others. Second pairing would haveto by Kyou and Tomoya since I can't help but love a good tsundere relationship. Aside from that, I wasn't so big on the other relationships, even though I thought Nagisa was adorable the entire time. As for my favorite non-heroine related combination, Sunohara x ANYONE period, especially in the VN. That guy just oozes out hilarity and still tends to have these intense serious moments where he can be quite profound.