I've never cared about any couple like I do Luke and Lorelai. For me they're soulmates and I thought so from their first scene in the pilot! I agree that the writers made them seem too different and annoyed with each other sometimes, but I think they're both outsiders in their own ways who trust and love very few. They're both their own worst enemy. Neither is a good communicator but both feel things a lot more deeply than they let on and I see them as very emotional and sensitive. Both distance and avoid, him with rants and by shutting people out and her by deflecting with humor and taking actions she probably shouldn't. Neither is necessarily smart in a bookish Rory way but both are actually very intelligent in their own ways. He's very competent, pragmatic, rational and has a knack for fixing things and she is extremely quick, clever, witty, creative and resourceful. The're both independent and determined to do things their own way no matter what they're told. They put up fronts that don't necessarily represent who they are - he seems more of a cynical people hater than he actually is and she seems more airy and lighthearted than she actually is - but both have very good but damaged hearts underneath that outer layer. I don't see them as completely opposite as some do and I do think they're delighted with and challenged by each other more than they're upset and confused even though I agree that the show didn't always do a very good job of showing that once they got together.
My favorite java junkie episodes before they started dating are Forgiveness and Stuff, Double Date, Donna Reed, Run Away, Bracebridge, Secrets and Loans, A-Tisket, Dead Uncles, They Shoot Gilmores, Thanksgiving, Poes, The Fundamental Things Apply, Clamor, Nag, The Incredible Sinking Lorelai, and of course the last few of season 4.
I actually like most of their relationship in season 5 even though I agree that we could have seen them more affectionate and smiley at times. I think they have some good scenes in Season 6 too, especially before we find out about April. The scene where Luke comforts Lorelai about Paul Anka and Rory and tries to convince her she's a good mom is amazing. I also love the finale in season 7.
After reading this thread I think I had a lot more I wanted to say but got too excited to remember!