Although they do not look alike, the Meganuron (a.k.a Meganulon) in this movie is based on the Meganurons that attack the villagers in the Toho monster movie classic, Rodan (1956).
Director's cameo: Director Massaki Tezuka is seen in a white shirt during a post ending credits sequence on a playground with school children. Post Ending Credits cameos are a kind of trademark of Tezuka's, as he in one in every Godzilla film he's directed.
Some of the footage from the original Godzilla (1954) was recreated with the new Godzilla suit, since Godzilla's appearance has changed so much from the original version.
The infamous "Giant Leap" Godzilla performs against Megaguirus during the final battle is a tribute to Godzilla suit actor Tsutomu Kitagawa's stuntwork in Toei's Super Sentai Series (featured as Dynaman (1988) and "Power Rangers" in the US).
Toho continued their tradition of casting actors from their science fiction films of the 1950s and 1960s. The character of Yoshino Yoshizawa is played by Yuriko Hoshi who had previously starred as Yoka in Mothra vs. Godzilla (1964) and as Naoko (a completely different character) in the sequel Ghidorah, the Three-Headed Monster (1964).