Heh, this is what I get for forgetting a topic I started. I figured I give my input anyway.
Ryuuji Takasu and Taiga Aisaka (Toradora!)
http://www.youtube.com/watch?v=a81hzmqVEZcWhat makes Ryuuji and Taiga special is their contrasting backgrounds and personalities, but not only that, the comedic manner in how they met. Since the beginning, you're expecting the two of them to end up developing feelings for each other, but you wait, and wait, and wait, and not until close to the end when it's at its sweetest does it actually happen, when they're honest to themselves and share the most sincere and sweetest of kisses in almost any anime I've ever seen. And it helps that they actually look good together too.
Okabe Rintarou and Kurisu Makise (Steins; Gate)
http://www.youtube.com/watch?v=kk69xGFTXuMOne word to describe Steins; Gate. Wow. It starts out as a comedy, but gradually become a tragedy, the back to an awesome happy ending narrative that if you're not paying attention, you miss something important. That brings us to Okabe and Kurisu. Quite possibly the wackiest pairing due to Okabe's claim to being a mad scientist and Kurisu's legitimate scientific knowledge, and their accidental discovery of time travel through the use of a cell-phone controlled microwave. Yeah, that kind of crazy. Without delving into spoilers, the two end up developing strong feelings for each other despite being literal polar opposites. Given the circumstances and the alternating timelines, they make for an awesome couple.
Kirito/Kirigaya Kazuto and Asuna/Asuna Yuki (Sword Art Online)
http://www.youtube.com/watch?v=rrl2dyJjyKkSAO is a big deal. It's one of the few anime that released in Japan that almost immediately releases in the US. Most of the time, an anime takes several years between releases due to the licensing and copyright-related paperwork that needs to be completed. Legal IP's aside, the couple of Kirito and Asuna would normally be cliche, if it weren't for the setting. It's the gamers' ultimate dream/fantasy, done in a way without coming off as overly nerdy or stereotypical. Yeah, some of that is there, but the execution is near-flawless despite the shortcomings. And to add to that they're forced to be trapped in a video game or die, and live to the best of their ability despite that morbid truth, and continue their relationship in the real world, shows the strength of their relationship.
Kei Kusanagi and Mizuho Kazami (Onegai Teacher/Please Teacher!)
(Sorry, no video this time.)
Talk about a blast from the past...sorta. Please Teacher is one of those anime that I would watch over and over again. Like some of the previous entries on this list, the premise of Kei and Mizuho is absolutely ridiculous. But it's that ridiculousness that makes this couple great. If you also had context and knew the in-story concept of Standstills, it makes the relationship even better, with every moment being more poignant and important, almost as if it were life and death, and in a way, it kinda is. Considering how much Mizuho is hit on due to her attractiveness, and Kei's underdog style, it makes for the ultimate dream couple. That, and together they're quite hilarious and it doesn't help that Kei is significantly shorter than Mizuho either.
There's a lot more, but the thing is, I could go all day listing off my favorite couples. I'll ask myself if I want to continue the list or not because it's going to take a lot of time for one, and a lot of text for two.