History: The start of the relationship was glorious and back in the first season they had a fairytale quality. They were enjoyable and so cute together... No fairytale is good enough though, without the bad witch. And in this case the return of Georgina Sparks served that purpose. Georgina used every possible way to make Serena's life unbearable and even if her friends stepped up and dismissed her, the lies she had told Dan and Dan's kiss with Georgina, really put a strain on their dreamy relationship, making it less dreamy.
They broke up for the summer, but Dan's inability to finish a story about their break-up, showed him that he and Serena weren't over. They made up again in a dreamy way and kept secret-dating for a couple of episodes. When their relationship got revealed by gossip girl, their close ones ( Rufus and Blair) stated that they should have resolved their issues before getting back together. Being closed in an elevator made them face the fact that the reasons they broke up in the first place were still very real and ended their relationship.
The meddling of Blair and the minions (and Chuck as we found out later in the episode) at school made it impossible for them to be friends without arguing. After spending a considerable amount of time apart, they met outside Nate's house and decided that they were mature enough to be friends again. Serena, then, run into Aaron, an artist from the gallery with whom she had been married when she was eight, and they started dating. Bart's death brought Dan and Serena closer together and her and Aaron further apart. Rufus and Lily's possible reunion prevented them from getting together before the Christmas holidays, but when they got back to school, they decided to reunite. The reveal though that they shared a sibling was too much to handle so they broke up again.
Season 3 had almost nothing Derena related, except the season finale that showed that what they had, didn't vanish. Back then, Serena was with Nate and Dan with Vanessa, when Serena's family problems led her to turn to Dan for help. They spent the night together and shared a kiss. Jenny, though, took a photo of them sleeping on Dan's bed and sent it to Gossip Girl. Nate found out and sent a photo to Vanessa who wasn't in New York at the time. The season ended with Serena trying to choose between Nate and Dan, while Dan wanted to go to Paris to tell Serena he loves her, only to be stopped by Georgina telling him they had a son together.
On the beginning of season 4, Dan was busy dealing with being a father to his son with Georgina, which didn't exactly make Serena his first priority. When it turned out that Milo wasn't really his son, he got back to claiming Serena, while she still hadn't decided who she wanted. Serena finally decides that she wants Dan in the middle of season 4 and Dan is extremely supportive of her, when Juliette's schemes make her seem like a drug addict. The reunion didn't last long this time either, since they weren't clearly ready to commit in a serious relationship. So they decide that the next time they get together, it will be forever.
Shortly after, Serena started dating Ben, the professor in the boarding school that her mother falsely accused of abusing Serena. Dan started spending time with Blair and after kissing her, he realised that he was in love with her. Serena and Ben broke up at the end of season 4 and during season 5, Serena started to realise that her relationship with Dan was the most important in her life and she now has fallen for him again. However, Dan is still in love with Blair and despite Serena's confession of love, he still seems quite invested. At this point, Serena is mad at Dan and Dan is rather indifferent. What could the future hold?
Conclusions: When Serena and Dan started dating they were so beautiful together. They faced their problems and solved them in the most decent way. That was until Georgina barged into their lives. Serena started lying to Dan and didn't trust their connection. I have to admit, it wouldn't be the easiest thing to tell but lying to him certainly led to their first break-up. Dan tried so hard to convince her to tell him the reason she was acting so weird. And by the time she was ready to tell him, he was tired.
In season 2, right after their second break up, Dan was the one who didn't trust Serena. He practically doubted her character, equating her to the spoiled upper east side girls. And this impacted her greatly and made her question the person she wanted to be. Once they could be friends again and after Bart's death it was clear that however good Aaron has been, he couldn't possibly be compared to what Dan meant to Serena. The reveal that they shared a brother turned out to be unbearable to them and thus led to the end of their relationship.
The finale of season 3 was indicative that no matter how far they seemed to be, they were still closer with each other than with the people they were with. As Blair recently revealed us, there was no choice to be made, Serena always knew she wanted to be with Dan. She was just afraid. But Dan didn't know that. He didn't know that the reason it has taken months for her to choose him was her fear.
I think that the moment that was decisive of Dan's ignorance to Serena right now is this discussion with Blair from 4x11:
Blair:"I think I figured it out. Serena had an affair with her teacher because let's face it it's Serena and what else is left to do in Connecticut, then she came to her senses and discarded him like last season kno booties, then he became crazy stalker and Serena pressed charges. That should be warning to you Humphrey"
Dan:"Yeah, because the parallels are striking"
Blair:"Never to be realised, literary aspirations check, townie; you are from Brooklyn so check, giving up everything to become Serena Van Der Woodsen's stalker check. Face it Humphrey you are one of a tie away from Mr Donovan's territory."
Dan:"Yeah except of the fact that stalker implies one-sided, Serena does respond cause she chose me"
Blair:" Yes it was obvious this morning at the Ostroph center that Serena couldn't wait to be in your arms."
Dan:" For the record, I haven't given anything up to be with Serena"
Blair:" Oh, of course not. Besides your time and your dignity. You are sofering around, aren't you? And I'm just curious, when was the last time you wrote anything? And writing D loves S over your journal overnight doesn't count"
Blair showed him that he was practically stalking her, revolving his life around her. And she was partially right. He hadn't written anything and he had spent the entire season pursuing a woman, who wasn't even sure that she wanted him. When Serena dated Ben, Dan was deeply hurt and having him living into his own house didn't make it any easier. The article Dan wrote about watching your love with someone else, touched even Blair. Therefore, Dan decided to move on.
Right now, Serena has finally decided that she wants Dan and only Dan. But she expected that everything would be just as it was before. She hasn't realised how last season has hurt Dan or how deep his feelings for Blair are. I don't know what the future holds for them, but I like the fact that Serena gets to pine for him for once.
And an answer to all the Dan haters. Of course, falling in love with her best friend is very bad, but we can't control our feelings. After all, they weren't together at the time he realised it and Serena wasn't treating him well either (bringing her current boyfriend to his house and being incredibly tactless). As for today, it might seem a little harsh right now, but at least he doesn't let her hope like she did with Nate last year. He's been straight forward. And finally, as most of you have noticed, his relationship with Blair only hurts his self-esteem and self confidence at the moment. He knows that no matter what he does there will always be Chuck in her heart. He is being selfless even though it might hurt him. And along with that, he is descent enough to be clear with Serena. Because how would it be better if he was telling her he loved her (which I think he does, some things don't just go away.) while he still has feelings for her best friend. His only fault is that he has fallen for her best friend.
That's not to say that Serena is the bad one in my eyes. I'm really sorry for her right now, but I can't help thinking she has taken Dan for granted all this time and hasn't considered her own mistakes. She doesn't deserve what happens right now, but none of them do. Dan doesn't deserve sacrificing everything for someone who needs to be reminded to thank him. Chuck doesn't deserve being put on hold and losing the woman he loves after all the progress he's done. Blair doesn't deserve losing her baby and torturing herself over a pact with God but she actually is the one that can put an end to the misery of all of them by finally deciding what she wants to do. If she wants to be with Chuck, she should do it. If she wants to be with Dan she can do that too. Sometimes, I wish that this square would be over, even if it wasn't the way I would have opted. I know it's a drama, but they are all so sad right now...