In order to reduce clutter and spoil jokes, this document will contain
all less than obvious references.

Episode 01

8:28 - She is referring to her period here
8:51 - Male semen is said to smell like squid
10:48 - 3-P can be interpreted as a threesome

Episode 02

14:23 - The Japanese word on the test is the word for "pencil"

Episode 03

13:36 - Shino is making a Haiku here.

Episode 04

10:17 - In Japan, a cherry is another way to say a virgin.
11:16 - Cool Biz - A campaign to help reduce electric consumption by limiting use of air conditioning.

Episode 05

5:32 - She believes men are horny when they're tired.
9:27 - My little sister's going through puberty is a manga from the creator of Seitokai Yakuindomo.
18:00 - Bread (pan) = panties so a glimpse of bread could be a panty shot.

Episode 06

0:00 - The band featured is the same group which sings Seitokai's OP
0:00 - Queen Records is a parody on the Japanese distribution company, King Records.
0:00 - King records child company, Starchild, distributes Seitokai Yakuindomo.
0:00 - The removal of the kittie masks is a reference to the OP of Highurashi no Naku Koro Ni.
11:46 - Okazu can refer to a side dish, or a object of desire.
15:48 - 1x9 (in-ku) pronounced as "iku" means "I'm cumming."
18:30 - Drawing the character for "person" on your palm and gulping it is a charm should provide confidence.
19:50 - Tebura is when you cover your breasts with your hands only. Primarily it means to come empty-handed.

Episode 07

4:43 - "Hameru" means to insert in. In this case it means to have sex.

Episode 08

3:24 - She covers up the "high" from high school, making it "Full-nude girls horse riding" this time.
3:42 - "self charge" is to masturbate.
4:03 - "Paiotsu" is a word play on "Oppai," which means boobs.
6:14 - This sign could also mean "doggy-style position" in this case.
12:42 - "Kainin" can mean both dismissal or pregnancy.
12:54 - "Kaku kaku, jika jika" is an expression similar to etcetera,where the "shiko shiko" version expresses the sound of a man masturbating.

Episode 09

9:24 - "Putting up a tent" is a slang term for getting and erection.

Episode 10

15:00 - Chinchin is a term used for penis (slang), but is also the name of a trick where the dog sits up on its hind legs.

Episode 11

11:25 - Although priced at 4935 yen each, a Blu-Ray on amazon is actually less than 4000 yen each after discounts.
11:34 - 721 sounds like the word for masturbation
18:48 - She meant to say "Seiheki" (tendency), which he mistook for "Seieki" (semen).
19:28 - This is a parody on the site niconico, where users may comment on videos, and their comments scroll across the screen.

Episode 12
17:08 - As before, 3 P means a threesome
21:23 - "19" sounds like "I'm cumming"

Episode 13

5:21 - A gold license is a license with a golden highlight over the expiration date to show a good driving recrod.