Okay, in the End of Evangelion, it showed only Asuka and Shinji, correct? If you thought that, you'd be wrong. If you had payed attention, before it showed them, he had decided that he wanted everyone to live again, so people started appearing in the LCL that they had turned into. The reason it showed Asuka and Shinji is because the creator wanted to show Shinji finally being able to express how much anger he held toward Asuka for all the crap she put him through.
(don't ask, I read a huge analysis of the whole ending... it was the only way I could understand it.)
I know I was like huh? Asuka was alive that meant Shinji had feelings for her. no one else was there....and the ending to th series was very pivotal and climaxed(ah the raw vulnerability of the human mind and heart) but the ending the one with Shinji standing with everyone in a circle round him...that just ended in total crap.
Huh, I always took the claping thing as everyone, (Which they state) Congradulating Shinji. For what is the actual question- I think it's because he reilized that he friggin' controls his emoutions and actions not other people makin' him- my little sister knows this of course but eveidently it took Shinji 26 episodes. biggrin
Oh, and the Belly button thing- Honest to God never really thought about it... But now I am! AHHH!