Vert gives us a now-outdated reminder to preorder Hoop: Reach. (It wasn't out yet when the original Japanese version of Neptunia was released, but the English version came out at least a year after the title being bland-named had already been released.)
One of the first few lines Neptune has is, "Neptune does what you all don't," which is appropriate since Sega, which Neptune represents, used "Genesis does what Nintendon't" as an advertising line back in the day. What's more, this was a purely American ad campaign; the translators were actively adding to the shout outs, even obscure ones that many kids today likely wouldn't know about.
Gamindustri's preferred social networking site is Chirper.
When gaining a level, Neptune may occasionally hum the victory tune from Final Fantasy.
5pb provides the voice for a synthesizer, but becomes upset that people are making her sing and dance to rather strange things.
MetalDogoos are hidden in a single group of enemies in LAN Castle. They're worth about 4 times the Experience and twice the Credits as the rest of the fight, and their Metal Jelly sells for another 11111 Credits.
Vert's Military Dress costume adjusts her color scheme in such a way that she looks like Luka.
In a Chirper event focusing on Nisa, Blanc is reminded of a game where the main character is part of a secret Broadway troupe living in New York. The game in question is Sakura Taisen V, which was released by NIS America.
Blanc mentions that she likes ordering books from Blarnes and Foible (Barnes and Noble).
The first time the group meets Linda (a thug working for ASIC and a recurring annoyance throughout the game), they mock her "soldier" title and tell her she's nothing more than an "underling" (perhaps even a Mid-Boss?) Just as in Disgaea, Linda's on-screen title changes to reflect this, and it sticks with her for the rest of the game.
One of the random chirpers in Lastation is named Nana Kimizu and looks like Nana Mizuki.
Nisa's entire second chirper event is one big reference to Kaiketsu Zubat.
There is a quest given by a "UniSound-Alike". She needs you to kill a few Cuberials who tricked her into taking on a curse to make a wish. Another quest is given by a "Small White Animal" who has made so many contracts with young girls that it needs you to go out and get it some more magical contract paper.
In Chapter 7 a new NPC that looks almost exactly like Kyubey in shows up in Planeptune named Rokubei. It wonders why you'd be asking it about a contract and insists that it's just a cat.
When Nepgear is talking with Vert about how she's no longer the main character like she was in the last game, Blanc comes by to inform her that she has Dragonball Syndrome, where the older family member passes the lead role to a younger one only to steal it back and that it can only get worse from there for the younger character.
When Plutia is about to transform to give Noire her "most popular lecture" in chapter 3, Neptune tells the player to "Press the B Button to stop the evolution" (Well, in the Japanese version, at least.)
In episode 3, when Neptune and her friends looking up for Vert, one of her collection figures surprisingly resembles Gintoki.
In Episode 3, the aerobatic display team at 5ob's concert is called Green Impulse, clearly a shoutout to Blue Impulse, the JASDF's aerobatic display team, down to their color patterns and aircraft. (Minus the Vert ita-trainer.)
Still in episode 6, Neptunia poking fun at Noire's proud assertation that her systems were the best in the world is an obvious nod to Rudol Von Stroheim's catchphrase from the second part of JoJo's Bizarre Adventure, which David Production animated prior to Neptunia. Just to make it more obvious, they added in visual onomatopoeia, a hallmark of Jojo.
In episode 7, Pirachu takes the infamous Lupin Dive. From the same episode, Neptune can be seen playing Mugen Souls Z.
In episode 8, when Nepgear unintentionally become a nudist, Vert pulls the "Just as planned" expression.
In episode 11, Iffy is shown running down the stairs of the Basilicom with Histoire in a scene very reminiscent of the climactic scene from Puella Magi Madoka Magica. Bonus points for (spoilers for both series!) Tari looking and acting a lot like how Walpurgisnacht did in the anime proper.