My friend and fellow Clouffie devotee Kristel outlined the best hints and moments from Advent Children while we were discussing it on Livejournal. I don't think I could put it any better, so the following section was written by her:

This goes hand in hand with On the Way to a Smile.

In OTWTAS, we learn that Barret, Tifa, Cloud, Denzel, and Marlene were all staying together, kinda as a family. Barret runs off to take care of things, and man I need to re-read this cuz I forget the details but Cloud basically is Tifa's go-fer for supplies for her bar. While he's out and about picking up stuff for the bar, he comes across people needing odd delivery jobs, and he starts taking them on the side for some extra cash to supe up his bike, behind Tifa's back. He ends up taking on a delivery of flowers from Aeris' mom to I guess the lost city, and it gets him all uber depressed, so he really starts spending long periods of time away from "home". Etc etc, until one day Tifa gets all pissy etc uhhh and eventually Cloud spends some time at home cuz he likes hanging out with Denzel.

Well all that time he was staying away from home, he was really staying in the church. Tifa doesnt know that, hence her "I guess so" whenever Marlene asks if Cloud lives there.

Now, when Tifa and Marlene are scoping out Cloud's pad, they find a big box of materia, and there's a little eyebrow raise at that, I believe.

Now fastforward halfway through the movie. Yuffie drops in and asks WHERE'S MY MATERIA??? OMFG HER MATERIA CLOUD HAD HER MATERIA SO SHE MUST'VE BEEN STAYING WITH CLOUD SOME XDDD

The other huge thing with AC was in Reminscence of FF7. YUFFIE of all people is calling to harass Cloud. I first heard her voice and was laughing at Yuffie, then I had to stop myself and think "No, wait, shouldnt that be Tifa??" Hehe. But yes. She even bugs Barret and Cid and Vincent enough to try to track down Cloud.

And what happens when Cloud arrives? He's got a package from none other than YUFFIE. And what does he do? Wait to open it? Nah, he rips right into it "What's the hurry??"

AND IT'S A FREAKING "CLOSED FOR BUSINESS" SIGN XDDDDDDDD WINK WINK NUDGE NUDGE

But of course Cloud has to piss me off and call TIFA to see if she can get time off so they can go do something with the kids. WTF. MARLENE HAS A DADDY, CLOUD, HIS NAME IS BARRET. NOW GO SEX YUFFIE ALREADY :/

Also:

Dontcha think it's just a LITTLE odd that Yuffie would VOLUNTEER her materia to ANYBODY??? *winkwink* *nudgenudge* That "Cloud, I brought you materia!!" line just holds SO much depth XD