What is the meaning of the title "Bad Apple", and which characters appear? The original video for Bad Apple!! is one of the most well-known Touhou videos. Here's the original, together with English subtitles:

http://www.youtube.com/watch?v=VzEUeWnV73U

Why is the song called Bad Apple? There is an apple in the video but I don't imagine that's why. It matches the lyrics decently, but it still seems like a strange name for a song.

Also, all of the characters in the video are black and white silhouettes. Which characters are represented and in what order?
The song "Bad Apple" was originally the stage 3 theme from Touhou 5 Lotus Land Story. The popular version by Alstroemeria Records is a lyrical remix of that. Because Elly was the boss for stage 3, she makes an appearance towards the end of the video despite being a minor character. 

There isn't any real explanation in the game as to why the song would be called "Bad Apple". Many original Touhou music pieces have names that don't really match the plot in any way, and as far as I know ZUN has never specifically explained this title. However, it is true that the popularity of the remix may be in part because it casts the series in a somewhat darker and more serious tone than the ordinary moe artwork, as the name would suggest.

As for the characters, I'll list them in order of appearance. The times correspond to when they first appear, and the names link to the relevant articles on Touhou Wiki.

0:00 Hakurei Reimu (博麗 霊夢)



0:15 Kirisame Marisa (霧雨　魔理沙)



0:28 Patchouli Knowledge (パチュリー・ノーレッジ)



0:36 Remilia Scarlet (レミリア・スカーレット)



0:45 Izayoi Sakuya (十六夜 咲夜)



0:50 Flandre Scarlet (フランドール・スカーレット)



0:58 Konpaku Youmu (魂魄　妖夢)



1:03 Saigyouji Yuyuko (西行寺　幽々子)



1:11 Onozuka Komachi (小野塚　小町)



1:18 Shiki Eiki Yamazanadu (四季映姫・ヤマザナドゥ)



1:25 Fujiwara no Mokou (藤原　妹紅)



1:32 Kamishirasawa Keine (上白沢　慧音)



1:39 Yagokoro Eirin (八意　永琳)



1:45 Houraisan Kaguya (蓬莱山　輝夜)



1:51 Prismriver Sisters (プリズムリバー三姉妹), from left to right, Lyrica, Merlin, and Lunasa



1:59 Chen (橙)



2:00 Yakumo Ran (八雲　藍)



2:01 Inaba Tewi (因幡　てゐ)



2:02 Reisen Udongein Inaba (鈴仙・優曇華院・イナバ)



2:05 Inubashiri Momiji (犬走　椛)



2:07 Kochiya Sanae (東風谷　早苗)



2:11 Kagiyama Hina (鍵山　雛)



2:12 Yasaka Kanako (八坂　神奈子)



2:15 Moriya Suwako (洩矢　諏訪子)



2:22 Yakumo Yukari (八雲　紫)



2:27 Hinanawi Tenshi (比那名居　天子)



2:36 Shameimaru Aya (射命丸　文)



2:41 Ibuki Suika (伊吹 萃香)



2:48 Alice Margatroid (アリス・マーガトロイド)



2:54 Kawashiro Nitori (河城 にとり)



3:02 Kazami Yuuka (風見　幽香)



3:09 Elly (エリー)



3:20 Hakurei Reimu, PC-98 appearance 



3:24 Kirisame Marisa, PC-98 appearance