We've all done it. We're watching/reading our favourite shows/books/whatever and there's always a pair of characters that you just KNOW are perfect for each other. Whether or not the creators agree with you or not is another thing...
Snake and Otacon - The Metal Gear Solid series.
Oh come on, like you haven't noticed the great chemestry these two have. Besides, who says 'ships necessarily have to be romantic? Why not bromantic? These two became instant best buds on Shadow Moses Island in the first Metal Gear Solid game, and at the end of Metal Gear Solid 4 Otacon vows to stay by Snakes side until he finally dies from his own genes. That right there is love, and these two share it.
Barney Stintson and Robin Scherbatsky - How I Met Your Mother
I was SO pissed when I saw what happened to these two. After building up their relationship, including a great friendship where they bounced off each other beautifully, what happened? Robin got stuck with that idiot Ted (who honestly, I don't think she had anywhere NEAR as much chemistry with) and Barney gets a daughter. Wow. Anyone who saw the interplay between these two KNOWS that these two are meant for each other. Both are witty, sassy, and the only ones thick-skinned and stubborn enough to put up with each other. I can't believe they broke these guys up.
Jeff Greene and Dicey Tillerman
The relationship between Jeff and Dicey is a special one to me. They are the exact opposite of each other, yet both are brought together by music and what they can give to each other - headstrong Dicey pushes Jeff, challenges him to be better and motivate himself, and Jeff can reel Dicey back in when she starts getting a bit wild. Their relationship nearly fails when Dicey gets too headstrong and stubborn, thinking her way is the only way, but Jeff wisely steps back and lets her learn.
Harry Potter and Ginny Weasley
I've been cheering for these two ever since Harry saved Ginny from the Chamber of Secrets. Ginny finally got her hero, and Harry joined the Weasley family - how well does that work out? There's something romantic about staying true to someone until they finally realise it's you they want. Plus, Ginny's one of the few people in the world to actually be possessed by Voldemort - not just possessed mind, but confided in him and bonded with him until she figured out what was going on - and as such is one of the few people who can even begin to understand what Harry has been through.
Uzumaki Naruto and Hyuga Hinata
If Masashi Kishimoto stuffs this one up and puts Naruto with that stupid moron Haruno Sakura I will FLIP. Naruto was treated like DIRT by nearly all of the citizens of Konohagakure purely for being the unfortunate soul who happened to house Kurama, the Nine-Tailed Fox. Only Hinata loved and respected him, looking up to him and even adopting his ninja way in never giving up and never going back on her word. Not to mention when Naruto was getting his butt handed to him by Pain trying to save Konoha, there was only one person game enough to step in and protect him, even though she stood no chance and was 100% certain to die, and that was Hinata. Not Sakura (who was one of the ones who looked down on Naruto), Hinata.