In the first episode the name of one of the crew members aboard the the stricken research vessel is Doctor Meddings. This is a homage to the original designer of the Thunderbirds crafts - Derek Meddings.
In Episode 8 of Series 1 - Eos - there is a reference to 2001: A Space Odyssey. It is a failure of the AE35 unit which is part of the communication system of both the spaceship Discovery in the movie and Thunderbird 5 in the show.
During the credits at the end of each episode, one of the pictures shows an artists sketch of the Tracy Island lounge, but with the five portraits from the original 1960s series on the wall instead of the new portraits.
In 'Breakdown' International Rescue pretend to forget Virgil's birthday. Virgil says his birthday is on August 15th. When Virgil asks John what day it is, John says Sunday. According to official calendars, August 15th in 2060 is a Sunday.
First episode had many references from past Gerry Anderson TV series. Stingray was shown, Sealab I had the front design of the Eagle space transporter from Space 1999 and the ship at the end was called the Shadow which was the name for the secret organization in UFO (SHADO - Supreme Headquarters Alien Defence Organisation).