References that I have loved in the shorts and in the series:
"Slacker Breaker!" Nyaruko, in the first short series
"Do you remember our love?" Kuuko in episode 2. (I am hoping the DYRL BD has English subtitles so I can really fully enjoy that reference.)
Kuuko forced to play Pisces in make-believe Saint Seiya in space kindergarten(same episode as the Slacker Breaker)
"Let's go to the Grand Line". Nyaruko, episode 2. Oh ho ho.
Atoko's and Nyaruko's silent elevator ride in the second short series.
I will have to remember to link to that site with all of the references.