Questions like this should be posted in the Who Forum. This is indeed a lot to ask because there's a lot of different anime in it, and questions like this usually take a group effort to cover everything. Because of the nature of the Who Board, only one person can get credit for answering a question. Therefore, the forum would be a better place for this, so more people can see it, and more people can contribute to identifying the characters/animes. Hope this helps.

And if you post in the forum, I'll be more than happy to help. As the Who Board mod, I just don't want to have to give credit to one person if multiple people help identify the anime in the video.

0:48 Ryuunosuke, Nanami, Misaki, Sorata, Jin & Mashiro Shiina from Sakurasou no Pet na Kanojo

0:51 Mashiro Shiina from Sakurasou no Pet na Kanojo

0:55 Sora & Haruka from Yosuga no Sora: In Solitude Where We Are Least Alone

0:57 I think Ryuunosuke's Computer Program from Sakurasou no Pet na Kanojo

0:58 Yuuko Aioi from Nichijou

1:01 Minami from Baka to Test

1:03 Yuuko from Baka to Test

1:04 Yuuji from Baka to Test

1:05 Kouta from Baka to Test

1:06 Toshimitsu from Baka to Test

1:08 Nishimura from Baka to Test

1:09 Akihisa Yoshii from Baka to Test

1:12 Some Bakuman Characters

1:15 Honoka Kousaka from Love Live School Idol Project

1:21 Inori & Shu from Guilty Crown

1:22 L & Light from Death Note

1:32 Victorique de Bois from Gosick

1:32 Makoto Tachibana from Free!

1:33

1:34 [url=http://myanimelist.net/anime/18507/Free!]Free!

1:38 OreImo

1:40 Chuunibyou

1:44 T.Araragi from Bakemonogatari & more Monogatari's

1:45 ?

1:46 Free!

1:46 - 1:55 ??????

1:56 Baka to Test

1:57Date A Live

1:59 Nichijou

2:06 Hyouka

2:08 Suzumiya Haruhi no Yuuutsu

2:09 Toradora

2:11 Nichijou

2:18 K-On!

2:20 Boku wa Tomodachi ga Sukunai

2:26 Hataraku Maou-Sama!

2:29 Nagi no Asukara

2:33 Free!

2:34 Hentai Ouji no to Warawanai Neko

2:35 Free!

2:36 K-On!

2:37 Free!

2:39 Black Rock Shooter

2:41 Fate/Zero Cafe (?)

2:43 K-On!

2:47 Toaru Kagaku no Railgun

2:50 Fate/Zero Cafe (?)

2:52 Nichijou

2:54 Toaru Kagaku no Railgun

4:04 Error can't find KurosakiIchigo

Well, thank you for all the hard work KurosakiIchigo!

In future though, Anon, this kind of thing really needs to go on the Forum instead.