Surprisingly enough, Naruto was the first to notice it. People don't give him enough credit, he's smarter than you'd think. It was the first time he knew something before Shikamaru, and he took pride in that. He didn't understand how no one else saw it, though. It was fairly obvious to him, right from the start.
The first time he noticed, was when Sasuke was late for training. Sasuke is never late.
"Teme, were where you?" he had asked.
Sasuke had shrugged, then gone over to a tree perfect for sulking under. That's when Naruto had seen that Sasuke didn't have his arms covered. It was weird to see him like that, with his incredibly pale arms crossed over his chest and black eyes looking up at the sky. It just wasn't Sasuke.
Then Neji appeared. His long dark brown hair was, as always, neatly brushed and out of his pale purple eyes, he wore the same clothes he always wore, he looked the same as he always did.
But completely different.
Why? Because he smiled at Sasuke. It was tiny, and very quick, but it was a smile none the less.
And if Naruto wasn't mistaken, Sasuke had returned the smile, only for an instant. Neji held something out to Sasuke, standing ever so slightly too close to him. Sasuke took it with a nod. It turned out to be Sasuke's arm warmers. He tugged the white things onto his arms and again gave Neji a fleeting smile, muttering something too soft for Naruto to hear. Neji nodded and walked off.
The second time he noticed, he saw the two boys in a dark corner of the supposedly haunted Uchiha compound. Naruto had gone to see if Sasuke wanted to spar, and wandered around the compound when he couldn't find him.
Neji was leaning against a wall, Sasuke was facing him. They where talking casually, smiling, and even occasionally laughing. They where standing close to each other again, and Naruto had wondered vaguely what Neji was doing there in the first place.
But then Neji did something. He touched Sasuke's face. All it was was a simple gesture, a thin pale finger grazing a pale cheek, very light and fast, but it was a touch. It wasn't a slap on the back or a friendly arm around the shoulders, it was more intimate than that. What Sasuke did in response was even more shocking to Naruto. He reached out and tugged on a bit of Neji's hair. Not to hurt the boy, it didn't make him pull away, but in a playful way.
Sasuke was never playful. And he never smiled like that when people touched him.
The third time he noticed was when he saw them on the roof of Sasuke's house. He had been running around the village, bored out of his mind, when he saw the two. Sasuke had been sitting leaned back, his arms supporting him as he looked up at the starry sky. Neji was cuddled up close to Sasuke, his arms around the other boy's thin waist.
So now, whenever Sasuke made excuses, was a little later or forgetful, he cut him some slack. Naruto was happy for his friends, and he would never tell until they where ready.
Even though he knew that no one would believe him when he said he knew first.