The Spaceship from Flight of the Navigator is still on display in the boneyard of the Studios Tour, or at least it was two months ago. In addition, pay attention in the prop room you walk through as part of the queue to the Studios Tour. You'll see a lot of stuff from Disney movies. Last time I was there I saw the jetpack for The Rocketeer, the large turkey and the shrinking machine used in "Honey, I Shrunk the Kids," a Binford Tools tractor, props from the old "Lottery Ticket" mini-movie originally played in the queue for the Backstage Tour, an audio-animatronic character in a balloon from World of Motion (I think), and at one time I saw the Hooter outfit from "Captain EO." Just take your time walking through that building, if they'll let you. It's amazing how much Disney history is in there.
The boneyard in the Tour also has a number of other vehicles from lesser known Disney/Touchstone movies like "Tin Men." If only the tour had more of this stuff and less figure-eighting to avoid that Lights, Motors, Action monstrosity...
Oh, yeah, and at the end of the Tour, the AFI Showcase usually has a lot of great movie memorabilia.
As for Journey Into Imagination with Figment, references to past Disney "inventors" abound. Ned Brainard ("Flubber"/"The Absent-Minded Professor") has an office, as does Dexter Riley. Weebo from "Flubber" is on display, there is a room marked "Flubber Storage," there are photos of Robin Williams as Ned Brainard and Rick Moranis as Wayne Szalinski, etc. Sadly, the queue is the most interesting part of the current incarnation of this attraction.
There are other references throughout the Parks. In Fantasyland, there is a shop called Sir Mickey's, which is based on "The Brave Little Tailor" and "Mickey and the Beanstalk" shorts (I've been told Willie the giant even looks in the shop from time to time). The Pecos Bill restaurant refers, to another Disney short about, naturally, Pecos Bill. And if you want to see a bit of "TRON," stop by Sounds Dangerous! in the Studios. After the show (which I like, thank you very much) you exit into an area that allows you to substitute your voice with the MCP, Mickey Mouse, Roger Rabbit, and a few others. It is very old and needing of updating, but it's probably the only place left I can think of that has anything "TRON" in it. I wish there were more.