What is the significance of the flowers that are placed on a student's desk after they leave Black class?

Question

So far on the series, every time a student is transferred out from Black class, different flowers are put on that student's desk the next morning.

Are these all flowers that really exist?
If so, what are their names and their significance?
And if not, what are they supposed to imply about each character?
What is the significance of each different kind of flower for each of the girls?

Answer 1

Yes, they are actual flowers. And according to this tweet from the anime's official Twitter account, the hanakotoba (花言葉, literally "flower words") that are hidden behind each flower have some relevance to each character.

See also: What is the relation between the flowers and the heroines in ED sequence of Photokano?

So far, the names of the flowers and their implied meanings have been stated in the manga or by the anime staff in response to viewer questions.

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Otoya Takechi

• ヤマユリ (yamayuri, lit. "mountain lily") / 「人生の楽しみ」 (pleasure of life) ¹

  
  ^{Photo by Wikimedia Commons user KENPEI / CC BY-SA 3.0}

Kouko Kaminaga

• 彼岸花^{1 2} (red spider lily)

  • 「また会う日を楽しみに」^{1 2} (looking forward to seeing you again)
  • 「悲しい思い出」² (sad memories)

  
  ^{Photo by Flickr user kenji mori / CC BY 2.0}

Haruki Sagae

• バーベナ (verbena) / 「家族の愛」 (family's love) ³

  
  ^{Photo by Flickr user TANAKA Juuyoh / CC BY 2.0}

Shiena Kenmochi

• アザミ (thistle) / 「復讐」 (revenge) ⁴

  
  ^{Photo by Wikimedia Commons user Qwert1234 / CC BY-SA 3.0}

Chitaru Namatame

• 赤バラ (red rose) / 「愛情」 (love) ⁴

Hitsugi Kirigaya

• 白バラ (white rose) / 「無邪気」 (innocent [childlike]) ⁴

Suzu Shutou

• 赤いチューリップ (red tulip) / 「恋の宣言」 (declaration of love) ⁵

Mahiru/Shinya Banba

• ヒルガオ (hirugao, Japanese bindweed) / 「絆」 (bond [human ties]) ⁶

  
  ^{Photo by Wikimedia Commons user KENPEI / CC BY-SA 3.0}

• ヨルガオ (yorugao, moonflower) / 「妖艶」 (seductive) ⁶

  
  ^{Photo by Wikimedia Commons user KENPEI / CC BY-SA 3.0}

Isuke Inukai

• 赤いカーネーション (red carnation) / 「愛を信じる」 (believe in love) ⁶

Sumireko Hanabusa

• アイスランドポピー (Iceland poppy) / 「慰め」 (comfort [consolation]) ⁷

  
  ^{Photo by Wikimedia Commons user David.Monniaux / CC BY-SA 3.0}

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References

<sub>1. 悪魔のリドル (2), ISBN 978-4-04-121056-7
2. https://twitter.com/akumariddleQA/status/460430373109788672 from the Q&A after episode 4
3. https://twitter.com/akumariddleQA/status/462962907437735936 from the Q&A after episode 5
4. https://twitter.com/akumariddleQA/status/468363714454773761 from the Q&A after episode 7
5. https://twitter.com/akumariddleQA/status/470574398374551552 from the Q&A after episode 8
6. https://twitter.com/akumariddleQA/status/475654677640384512 from the Q&A after episode 10
7. https://twitter.com/akumariddleQA/status/478499435496747008 from the Q&A after episode 11</sub>

Answer 2

It's a sign that the girl is 'gone' and not just absent.

The flowers on a desk usually means that the student is dead. However in the anime, it could mean that they were kicked out or worse, executed.