Everyone Is Jesus in Purgatory: Episode ten's ending, largely a homage to horror movies, caused one forum poster to conclude that Sakura is a bad parent.
Hilarious in Hindsight: When Tsuchida sees a "shooting star" in episode 2 and is supposed to make wish, he wishes for Dragon Quest VII to be released for the Nintendo DS. Six years and a generation of handhelds later...
Toy Ship: Koume and Yuu. Remember that these kids are in kindergarten.
You could take Kenji's fascination with Hii in this direction too.
And the fact that Hii gets easily embarrassed/flattered by his compliments - or about her relation to him in general.
Values Dissonance: No one ever seems to raise an eyebrow over the fact that a teacher knocked up his barely legal student, and ran off to America with her.
In Japan, the law states that the male has to be 18 or older and the female has to be 16 or older. In addition, anyone getting married under the age of 20 has to have the approval of the parents. In some foreign countries such as America, it can indeed "raise an eyebrow" but it is perfectly okay in Japan, though the students and teacher marrying may be a bit of a topic raiser.