Okay, I have seen about a million debates about who Naruto could/will end up with at the end of the Manga series and it amuses me to no end. However I have noticed that most of the time fans will ignore logic and the evidence given in order to back up their favorite pairings. So without further ado here is my impression of the 5 most likely Naruto pairings based on evidence I've collected from the manga.
(That's pairings for the character Naruto)
(There is actually 4, I could only think of 4 but I put 5 in the title 'cause it sounds better :L)
(Evidence is collected from the manga, not the Anime, which means none of the filler bullshit will be influencing my answers.)
WARNING: Contains Spoilers if you are not up to date on the Manga
Manga Chapter reference will be noted in [-] at the end of a bullet point.
Bullet points that show positive evidence for a pairing will be shown in color Negative bullet points will be black and neutral will be in white
So, In descending order, The 5 (4) Most likely Naruto pairings;
#4 NARUTO X SAKURA
From the very beginning of the manga series Naruto has made a point of having romantic feelings for Sakura and has asked her out on a date many time. 
However, no matter how persistent Naruto was Sakura continued to turn him down and express that she had no romantic feeling for him whatsoever; Calling him "Annoying" several times. 
As time progressed, their relationship to improved to the point that it is speculated that Sakura's feeling may have changed; as Yamato tells Sakura; "What really matters is the strength of your feeling for Naruto, Just by looking at you I can tell that you really-" 
However Yamato was cut off and never finished his sentence so there is no real proof that he could see feelings of a romantic nature. 
Naruto went out of his way to beat Gaara, surpassing his previous strength when Sakura's life was in danger. [132-138]
However it could also be considered that Naruto could have been fighting for Sasuke who was also down at this point, as vengeance for Lee, or just to make himself stronger. [132-138]
In times of high emotion Naruto will enter the Demon Fox Cloak, and in this fight, he keeps calm the whole time, suggesting that his emotions for Sakura, assuming he was in fact fighting for her, were not as strong as he himself thought. [132-138]
Sakura confesses to Naruto that she loves him, but it is revealed to be nothing more than a ploy in an attempt to stop Naruto from chasing Sasuke. And Naruto is very aware of this as he replies to the confession "I hate people who lie to themselves" which suggests that Naruto thinks or knows that Sakura would never feel that way about him or that his own feelings may have changed. [469-467]
#3 NARUTO X GAARA
Due to a state of high emotions; Naruto spent most of the time after the gaining the knowledge that Gaara was dead in Kyuubi form, expressing strong feelings for Gaara. [263-277]
However this could be considered to be strong feelings of friendship and a point is made that as a fellow Jinchuuriki Naruto empathizes with Gaara, but in turn that can also be interpreted as something that could make for romantic feelings, as Gaara and Naruto are one's that can truly understand each other 
When facing against Deidara; who killed Gaara Naruto's emotions took over him to the point that he went into Demon Fox Cloak; Two Tails. 
Gaara has made a point that his change in character is due to Naruto, talking about him on several occasions and expressing that Naruto made him question bonds, despite his personality and way of thinking previous to meeting him. 
#2 NARUTO X HINATA
Hinata has expressed unconditional love for Naruto from her very first appearance in the Manga. 
Naruto's naive and somewhat dumb nature made it so Naruto at no point realizes Hinata's feelings, however this is no indication as to how Naruto feels, and/or would feel if he knew. 
During Hinata's fight with Neji Naruto openly expresses concern for Hinata and urges her on, causing a grow in strength in Hinata. [78-80]
After Hinata's defeat, Naruto swears to avenge her stating; "Hinata, I promise you" 
When talking with Hinata, Naruto despite still being Naive to her feelings even after she expresses how she thinks he's strong and that makes her stronger, Naruto replies by saying "A person like you... I really like." 
During Naruto's fight with Neji it is highly suggested that he is fighting for Hinata, however his own reasons do play into the fight as well. [99-104]
When Hinata confesses her love to Naruto his reaction in that short amount of time told us basically nothing, even if he did show a great level of concern screaming "STOP!" as Hinata ran at Pein this could be taken in any context as Naruto does consider Hinata a friend none the less. 
After seeing Pein strike down Hinata and the assumption that she is dead, Naruto in a great state of emotion immediately progresses to Demon Fox Cloak; 6 Tails which is more than he has ever before had. And then Naruto progresses to 8 tails before having to have Minato repair the seal to avoid it breaking completely. This suggests that Naruto has never been so emotional and that he could in fact share Hinata's feelings. [437-440]
However the fact that his opponent, Pein, was also the one who killed his mentor Jiraiya, this could also play into the high level of emotion, but even if that is so, Hinata's confession and defeat is definitely the trigger.[437-440]
After Hinata's confession, despite gaining the knowledge that Hinata survived, Naruto has yet to talk to her about it all, going instead to continue his search for Sasuke, suggesting that Sasuke is indeed more important to Naruto and that he does not share her feelings, however this is inconclusive.
#1 NARUTO X SASUKE
From the very beginning of the Manga Naruto and Sasuke are shown to have strong feelings for each other in the form of a rivalry however this could easily be interpreted as something more than that, or in turn just a mutual hatred. 
From the very beginning Naruto and Sasuke are shown to have great influence on each other, seen driving each other on and causing each other to grow stronger. [018-019]
When fighting against Haku Sasuke, without thinking put himself in dangers way in order to protect Naruto, knowing full well that it could cost him his life, which is not something that the character previously portrayed would do. 
Thinking Sasuke to be dead, Naruto expresses a great deal of emotion, going Kyuubi for the first time ever due to it. [27-29]
Ever since that time, Naruto has gone Kyuubi whilst trying to protect Sasuke 
Whilst trying to stop Sasuke from leaving [227-233]
Upon meeting Orochimaru who has Sasuke [290-296] All of which are signs of incredibly strong emotion, getting stronger every time.
Ever since Sasuke left, all of Naruto's actions have been toward the goal of getting him back, Naruto constantly thinking of Sasuke, driving him on, to the point that Naruto can barely see anyone else, and that even his dream of being Hokage cannot be achieved unless he can save Sasuke.
All of this evidence can be considered both that of friendship and romantic feelings, and whilst we have to keep in mind that this is a Shonen Manga, not a romance and that it has always been labeled as Friendship, it can easily be considered something more, and the Manga itself has had several Yaoi innuendos so as a pairing they are not that surprising and based on all the evidence given, they're a lot more likely than any other Naruto pairing.
So there is the run down of who in my opinion, based on the evidence are the most likely pairings. I have made an attempt to be as unbiased as possible in this, which I can back up by saying that SasuNaru is not my favorite pairing and I'm completely against GaaNaru but that's what the evidence said to me.
Feel free to express your opinions on this matter and if you feel I've missed out any points then please point them out to me ^.^
Edit: *Re-posted because I wanted the skin x3 Is no longer up to date with the Manga as I am not up to date so please no spoilers xDD*