In the scene where Bill and Ted are addressing God, there are 2 statues at the base of the staircase. One is of Michael Powell and the other is of David Niven, an homage to Powell and Emeric Pressburger's afterlife classic Stairway to Heaven (1946). The stairway itself is the same as the one in that film, which has the USA title "Stairway to Heaven".
The guitar solo before KISS' "God Gave Rock And Roll To You", is performed by guitar legend Steve Vai The footage had already been shot and the world premiere was a week away, when he was asked to do it. He also contributed various music in the film, including "The Reaper Rap", which features on the end credits.
When Bill and Ted go to Missy's séance, you can see Chris Matheson and Ed Solomon, the creators and writers of Bill and Ted. They're the only men that are attending the séance. (Chris is the guy with the white shirt and Ed is the guy with the glasses.)
The "Riddance of Evil" book that Missy uses to send Bill & Ted to hell is actually a redressed copy of the Stephen King short-story collection "Four Past Midnight." She opens it to a page in the story "Secret Window, Secret Garden," which can be read clearly in a few frames of the film.
When Ted attempts to get into Heaven by proving himself worthy, he says, "Every rose has its thorn. Every night has a dawn. Every cowboy sings a sad sad song." These are the key lyrics of "Every Rose Has Its Thorn", a song sung by the popular 1980s/1990s heavy metal band Poison.
When Ted's father is taking de Nomolos away, Death says "Book em, Danno," made famous in Hawaii Five-O (1968). William Sadler would later go on to play the role of Jack McGarrett in Hawaii Five-0 (2010).
In the beginning of the movie, when Wild Stallyns is auditioning for Battle of the Bands, and when Ted is introducing the princesses, he says "...the beautiful princesses from medieval England...", and turns away from the mic at the word "medieval", trying not to expose their time traveling. However, the sentence segment that came just before that was "celebrating their fifth year in the Twentieth Century". Also, in the birthday party scene, the cake says "Happy 521st Birthday".
In a deleted sequence, the Evil Robot Usses use devices to re-create Bill and Ted's' Personal Hells (Granny Preston, the Easter Bunny, and Col. Oats) and send them after the heroes. Bill and Ted end up having to face their fears to get rid of them: Bill gives Granny her kiss on the cheek, Ted calls his brother and apologizes for stealing his Easter candy, and both boys treat Oats with kindness and friendship rather than terror.
The Evil Robot Usses were supposed to kill Bill and Ted at the Battle of the Bands, whereupon the boys would invoke their wins against Death to get resurrected. This part does appear in the comic book adaptation of the movie, which was based on an earlier draft of the script.
The scene in which Evil Robot Bill & Ted kidnap the Princess Babes to take them to the Battle of the Bands was notably different for several reasons. First, the robots knock Missy out, not with their breath but with Evil Bill's fist! In early drafts of the script, Captain Logan also confronted the robots, only to be pushed up into the ceiling by them. The robots then pull an outrageous bluff by unzipping their skins to reveal themselves to be disguised . . . as each other! (This would have tied in with Rufus' revelation of actually being Ms. Wardroe at the end of the movie.) If you look closely while watching the movie, you can see the discarded skins on the floor behind Evil Bill & Ted as they talk to Bill & Ted on the phone.