The Power Transfer
This is the climax of the T/Y storyline, and practically /everything/ about it is different in one way or the other in the anime and in the manga.
I've split this up in three: the setting for the power transfer (when and where it happens); the power transfer scene itself (everything that happens from the moment Yuki opens his eyes to the moment Touya falls asleep); and the events that follow over the next hours or days (depending on whether it's the manga or the anime), including The Talk Touya and Yuki have about Yuki's reality as a person (which is sort of also a confession, for Touya).
♥ Setting for the power transfer ♥
In the anime, Touya and Yuki's class is filming a movie at Eriol's house (Nakuru is the director). Of course Touya and Yuki are the stars (Sherlock Holmes and his nemesis, respectively). While they're filmng a scene in the balcony, Yuki faints and starts to fall over the railing, Touya manages to grab his hand, but it begins to fade away and his hold slips. Sakura uses Windy to break his fall and he's not hurt. They take him to a spare bedroom, and that's when the power transfer happens.
In the manga, Yuki faints during gym class, and Touya carries him to the infirmary. It's simpler, not as dramatic as the balcony thing, of course. I have to admit, I was ready to tear out myown hair when Yuki started to fall... I'm not saying it's /better/ though. There's something just irresistable about Touya carrying an unconscious Yuki in his arms.
♥ The power transfer itself ♥
Things in the anime and manga continue much in the same way: Yuki wakes up, Touya begins to tell him the truth about himself, they're interupted by Nakuru, who wants Touya to go back to class/filming. He finally tellsher that she's in the way, and after she goes, he tells Yuki that he knows he's not human and about 5 seconds later the fangirls begin squealing (I know I did).
This scene in the anime is wonderful. I especially love how, for a second, it looks like Yue is going to kiss Touya on the lips. Everything about it is well done, the music, the character's expressions, it's all great. But there is /one/ thing that is different in the manga, and that in my opinion, makes the manga more poignant.
In the anime, Nakuru bursts into the room, asks how Yuki is, and when he says he's okay, she sugests that they should get back to filming. Touya gives her a /look/ and chases her out of the room, telling her that she is getting in the way between him and Yuki and slamming the door in her face.
In the manga, Touya and Yuki are interrupted by Nakuru poking in through a window and, after asking if Yukito is alright, telling Touya to come back to the baseball test, because without them /both/ their team is at a disadvantage. And here is the fundamental difference: in the manga, Touya was originally going to go with her, but it was Yuki that stopped him. When Nakuru first tells him to come back, he says he's staying with Yuki; she tells him he'll get a 0 if he doesn't come and that everyone is waiting. So he agrees to go back, and tells Yuki that he'll be back as soon as it's over. Yuki agrees, already half asleep again. Touya turns to go, but something stops him. He looks down, Yuki has grabbed his shirt tightly, in an unconscious attempt to keep him from leaving him alone. He seems even more surprised than Touya to find himself hanging on to Touya's shirt so tightly, and Touya, after the initial surprise, /understands/.
So Touya turns back to Nakuru and tells her that he's not going, that he's staying with Yuki and that she's in the way, and then slams the window shut in her face and turns back to the business at hand. ^.~
In my opinion, the manga's version is better, because it shows just how important Touya is to Yuki, he doesn't even realize it, he simply reaches out for him, he simply needs Touya not to leave him alone. And perhaps Touya didn't realize before just how much he meant to Yuki, but with that one unconscious gesture, he /knew/, and then there was no stoping him, nothing important enough to make him leave Yuki's side, to delay even a moment longer in making sure that /Yuki/ wouldn't disappear from /his/ side.
♥ Afterwards ♥
I love the anime to bits and pieces, but you know, for the life of me I just could /not/ figure out how it was possible for Yuki to /still/ not know how Touya felt about him when Sakura confessed her feelings. Touya had all but admitted it earlier that day while they watched the movie, afterall. But what nagged me even more was this: what the /hell/ happened when Touya woke up?? Seriously. Touya has just given his power to Yue so Yuki won't disappear, there is nothing to keep them appart anymore, nothing to hide. And the way Yuki watched over Touya while he slept... excuse me, but if I had been any one of those two boys, everything would have come /pouring/ out the second Touya awoke. I mean...
...What is /wrong/ with those two??
And then I read the manga, and I found out that originally, Touya and Yuki weren't a pair of hopeless bakas. At least, not to /that/ degree.
The anime goes like this: power transfer - Yuki watches over Touya sleeping - Touya wakes up (and we know nothing about what happened, but I'm assuming Yuki was there) - at least a day passes - they have their little heart to heart as they watch the movie (when Touya tells Yuki that everything since they met is real and that for him it's enough to have Yuki by his side) - Sakura confesses her feelings for Yukito, and he tells her that he loves Touya but that he's not sure how Touya feels.
As opposed to the manga timeline: power transfer - Touya is asleep - Sakura's confession and Yuki not sure how Touya feels - Touya wakes up /while Yuki is there/ - the two of them have their heart to heart as soon as he wakes up (with much handholding and face touching absent in the anime).
Now /that/ makes more sense.
In that manga timeline Yuki doesn't come off as hopelessly clueless because of not being sure about Touya's feelings. Oh, one certainly assumes that he has to suspect that Touya loves him, but his doubts are perfectly reasonable: he just found out he's not human and that he's Yue's alternate form, /and/ he hasn't talked to Touya, he has no reassurance that Touya really doesn't care about all that. Having doubts is perfectly understandable in his situation.
Touya comes across as a lot less wishy washy too. One just /has/ to wonder how he could wake up and not say anything, and be content with that short conversation during the movie. But that same short conversation,which admittedly is still sort of beating around the bush, takes on a much more intense meaning when when he's tenderly touching Yuki's face. You /know/ that he's talking about love. The words might not be spoken, but their eyes speak more than elocuently enough. Plus in the manga we know that the first thing Touya did when he woke up was to say "Now you won't disappear", an important detail that was omitted in the anime. In fact, I simply don't undertand why they didn't just keep Touya's wake up scene in fact. It's one of the most romantic T/Y scenes, in fact it is /the/ scene in which the way they feel for each other finally becomes absolutely clear.