Tomoya and Sunohara in CLANNAD. Sunohara is definitely taking all the abuse, here. Tomoya doesn't really seem to care much one way or the other and most of the 'jerk' part of Jerk with a Heart of Gold comes from interactions with Sunohara. However, he really does care. Sometimes.
In Katawa Shoujo, Kenji gets on Hisao's nerves by constantly asking his to loan him money and his misogynist rantings (especially when they're targeted at Hisao's current girlfriend), but there are times when he appreciates having Kenji around, such as when he gets Iwanako's letter in Shizune's route and when he hears that Lilly is leaving for Scotland in Lilly's route.
Hisao and Emi often exchange playful insults in Emi's own route and in her close friend Rin's own.
Arihiko and Shiki in Tsukihime. Fighting until they're unconscious is just... well, there's no real ill feeling behind it, it's just what they do. Shiki doesn't even know why.
Arcueid and Ciel are also friends, which you might not pick up on since half the time they're trying to kill each other or something. Count the fact that Ciel is still alive yet isn't going after Arcueid 24/7 proof of Nasu's assurance that they're 'weird friends.'
In Halloween Otome: Seen with Mr. Bandages and The Count. Their constant bickering is obviously indicative of their deep-rooted affection and friendship for each other.