Clannad is probably my favorite out of the three, so far. The girls actually have a believable amount of intelligence, bar Fuko. While Kotomi is quirky, this is explained by her genious(eccentricity). Nagisa is typical moe, but she at least doesn't just go "Oh?" and remain useless like her other moe counterparts. Tomoyo and Kyou are extremely intelligent by Key standards. Plus the fact that it has awesome side-characters like Sunohara puts it ahead of the other two IMO. Biggest factor is that there's much less magic involved which is a big relief from all the stupid bullshit being crammed in your throat from Air and Kanon.
Clannad started off good for the first two or three episodes before taking a slight nosedive during Fuko's arc. She had a lot of funny moments, but she got a bit annoying and turned stale. Kotomi's route was full of moe and win. We've been hitting 3-way Nagisa/Tomoyo/Kyou arc with a bit of Sunohara route thrown in. I'm surprised they haven't fucked it up(Although Tomoyo/Kyou fags will say it's fucked up if he doesn't end with either). It has less forced BAWWWW moments than Kanon(+ or - depending on your own opinions) and instead seems more heart-warming. Seems he's going to end with Nagisa, but that's fine by me seeing as she was my favorite from the start(Tomoyo close second). Opinion subject to change. Although I can't see anything other than it being forced(A la Kanon).