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Green Lantern's Emerald City incorporates the ELO spaceship as part of its design.
The Beatles can be seen at "Planet Krypton"—sort of. From the knees down. There was also an attempt for Sgt. Pepper Humongous Mecha in the final battle scene, but that reference is nearly too subtle, even with annotation.
In the same panel as the Beatles, Tommy and the Acid Queen can be seen at the far left of the panel.
One of many cameos, a Background character in the gulag battle was visually baised on XO-Manowar of Valiant Comics. At around the same time as Kingdom Come was being published, Mark Waid was also signed on the write the Acclaim Era Reboot of the character, XO-Manowar: Rebirth.
While Magog is mostly based on Cable, he has elements of other Rob Liefeld characters as well. Most notably, his helmet is based on that of Shatterstar's with the addition of horns.
The center section of the Gulag is designed to look like the Hall of Doom from Challenge of the Superfriends, and the UN building looks like the Hall of Justice.