Two characters, Woz and Jobs, are named after Steve Jobs and Steve Wozniak, the creators of Apple.
Jobs even looks the part, having the sufficiently similar appearance to real Steve Jobs. Woz... well, if you squint really hard and discount his fashion sense.
Gidget and Moondoggie are named after characters from the Gidget book/TV/film series who have the same relationship. Mondoggie's real name, as stated on his pilot license, is James Darren Emerson — a composite reference to the actor playing the original Mondoggie role, James Darren, and Darren Emerson, a noted electronic musician.
Episode 20 features a prison called "Dabu Ghraib".
Shout outs to classic giant robot shows out the wazoo.
The three annoying kids are designed after the three annoying kids from the original Mobile Suit Gundam.
Their names are references to both Ray Charles, the Jazz musician, and keeping with the series' less prevalent architecture motifs, Ray and Charles EAMES were a married pair of famous modernist architects.
Anemone is a violently insane genetically altered Tyke Bomb in a red & black version of the hero's mech, similar to the situation with Zeta Gundam's aptly named Psyco Gundams.
Several elements of the plot & characters resemble elements from Gundam X, though this may be coincidence.
The key comparison is how the lead characters, notably Renton Thurston and Ikari Shinji (boys, both 14 years old) in the first episodes both end in a cliffhanger where the leads are in mortal danger: Evangelionís end while Shinji is in the thick of the battle while Eureka Seve Nís end with Renton joining the fray.
Renton's LFO toy is similar to Popy's and Bandai's late 1970s and early 1980s Chogokin ("Super Alloy") diecast toys, including blocky Off Model design and Rocket Punch spring-loaded fists.
Greg Egan, aka Doctor Bear, is a reference to two science fiction authors, Greg Egan and Greg Bear.
Renton is named after Mark Renton, from the movie Trainspotting. Similarly Diane Thurston, Renton's sister, is named after the character Dianne Coulston of the same film.
Warsaw is also known as "The Joy Division". Warsaw is the name the band Joy Division previously went by.
For The Movie, Peter Pan is mentioned at least 3 times and Renton and Eureka are even called "Peter and Wendy".
Gekko-go's gunner and owner, Ken-Goh, is a reference to Kengo Watanabe, an old buddy of the series chief scriptwriter, Dai Sato, with whom he also manages an indie electronic label Frogman Records.
Various Humongous Mecha designations in the series are mostly taken from the synthesizers' (mostly Roland) model numbers. The Devilfish is a famous mod for the Roland TB-303 that vastly expands the tonal capabilities of the synthesizer
Whenever members of the Gekko use codenames, they use characters and such from Alice in Wonderland.
Frank Lloyd Wright's Falling Water seems to have found an odd home in the depths of a mine.
A character named Lloydwright appears a few episodes later as a contact of Charles and Ray.
Renton's father Adroc Thurston seems to have been named for Adam "Ad-Rock" Horowitz of the Beastie Boys, and in one episode he's said to have worked with Drs. Yauch and Diamond (Adam "MCA" Yauch and Michael "Mike D" Diamond).
The Second Summer of Love is an event in the series that could potentially destroy all life. It's named after a time in '88 when European music attitude and composition was fused with the budding American techno and electronic, opening up new music and ideas for the 90's and beyond.