Disneyland is full of these to former attractions. To whit:
In The Many Adventures of Winnie the Pooh, just as you leave the Heffalumps and Woozles part, if you look behind you, you can see three trophy heads - Max, Buff, and Melvin, from the attraction that once occupied that spot: Country Bear Jamboree. In Florida, at Walt Disney World, turning around at the right moment you will be able to see a picture of Mr Toad handing over a deed to Owl as an homage to Mr Toad's Wild Ride which used to occupy that space.
Somewhere in the projector room in the queue for Indiana Jones Adventure, there is an Eeyore sign - that spot used to be the Eeyore section of the old parking lot.
In Autopia, there's a bronzed Midget Autopia car, referencing the long-gone attraction.
Swiss Family Treehouse, based off of the movie Swiss Family Robinson, once occupied the spot where Tarzan's Treehouse is now. A gramophone in Tarzan's Treehouse still plays the Swisskapolka
The Mighty Microscope from Adventure Thru Inner Space is still there - you can see it across from a mechanical arm that almost hits the Starspeeder 3000 in Star Tours and the comet scene pays a subtle nod to the snowflakes from Adventure.
The new Star Tours once again features the Mighty Microscope on left hand side of the screen in a lit corridor just before the Starspeeder 1000 leaves the unfinished Death Star 1 through a docking bay.
An actual engine from the Mine Train thru Nature's Wonderland sits at the edge of the Rivers of America
Mike Fink Keel Boats transported guests along the Rivers of America until 1997. One boat, the Gullywhumper, is moored as a prop along the rivers.
There are four shout-outs to the House of the Future in Innoventions alone.
Google's Wave service was named such because that's what communications were called in Firefly. The crash message is even Wash's infamous line "Curse your sudden but inevitable betrayal!"
The MEDLI (MSL Entry, Descent, and Landing Imager) instrument on the Mars Science Laboratory mission may be a reference to the character Medli from The Legend of Zelda: The Wind Waker. It's certainly possible, given the Zelda series's widespread fanbase and the relative age of most of the Jet Propulsion Laboratory employees.
In addition, one of the macrocycle inhibitors of the gene sonic hedgehog continues the reference. It is named Robotnikin.
Likewise, a retinal protein was named Pikachurin, due to its relation with electrical signals.
The POK erythroid myeloid ontogenic factor was originally named Pokémon, until Nintendo threatened legal action. Why? It's a master switch for cancer. It's given a generic name of Zbtb7
All of the elements after plutonium, once they are actually synthesized, are named either for a famous scientist (einsteinium, bohrium, mendelevium, nobelium, rutherfordium) or an important location, usually the element's "place of birth" (berkelium, californium, americium, darmstadtium). An abandoned mine at Ytterby, in the Stockholm archipelago, has four elements named for it: erbium, terbium, ytterbium and yttrium.
A lot of taxonomic names end up being Shout Outs to things. Often it's to the scientist who discovered it or to the location it was discovered, but there are some more unusual ones:
Interesting story behind Utahraptor spielbergi — scientists felt the raptors in Jurassic Park were too big, so when they did find ones at that size they named the species after the movie director. Velociraptors were about four feet tall. The filmmakers didn't think that would be scary enough and beefed 'em up. Sadly, though, Spielberg's lawyers rejected, so it was renamed Utahraptor ostrommaysorum, after John Ostrom, who discovered Deinonychus and established the dromaeosaurs as a family in the progress, and Chris Mays of Dinamation, which funded the expedition that discovered Utahraptor.
Han solo — it's a trilobite. It has a double meaning, actually, as Han refers to the Han People of China, and solo is a reference to this being the sole species of the Han genus, but the author who named it also wanted to make a Star Wars shout-out.
The scientific name for the dinosaur Masiakasaurus is Masiakasaurus knopfleri — the expedition crews were said to be listening to a lot of Dire Straits at the time. Mark Knopfler himself once made an amusing self-effacing comment about how appropriate it was to have a dinosaur named after him.
Cthulhu has two species named after him, a spider Pimoa cthulhu and microbe Cthulhu macrofasciculumque (whose flagella give it a vague resemblance to the tentacled god.)
At one time there used to be an eastern Iowa restaurant named Shipoopi's. note The musical takes place in Iowa and the playwright was a native Iowan.
Celestial bodies are also often named for real or fictitious people, in a tradition dating back to antiquity when planets and constellations were named for the gods.
A scientist named a rock in the Main Asteroid Belt 18610 Arthurdent". Later, another asteroid was dedicated to the author: 25924 Douglas Adams The naming of 25924 Douglasadams is itself a heartwarmer. The provisional name for it was 2001DA42. note The year in which Douglas Adams died, his initials, and the Ultimate Answer to Life, the Universe, and Everything, in that order. The only comments that could be given were along the lines of "it was sort of made for him, wasn't it?"
Asteroid 99942 Apophis. Even funnier, there is a small chance that the asteroid may hit Earth in 2036, so Apophis is our real-life enemy. (The name Apophis comes from Egyptian Mythology, but the asteroid's discoverers are said to be fans of Stargate SG-1.)
There's even one named after the fictitious Czech genius Jára Cimrman. Let's just say that the name of every other asteroid is a reference to something-or-other (since it's the discoverer who proposes the name, and there are few restrictions on the name choice.)
White dwarf BPM 37093 in the sky with a crystallized carbon core (read: diamond). Informally named: Lucy.
The dwarf planet now known as "Eris" was nicknamed "Xena" for 2 years while a final name and designation were decided. Its moon was officially named "Dysnomia" (Lawlessness) as a shoutout to actress Lucy Lawless.
Originally Colbert was competing for the naming of a space capsule, the name in second place wasSerenity.
Lucy, the fossilized Australopithecus named after the Beatles song "Lucy in the Sky with Diamonds".
Iron Maiden's drummer Nicko McBrain owns a restaurant, Rock N' Roll Ribs. The menu is filled with references to his band (such as "Appetite of THE BEAST", and the temperatures of sauce: Mild, Medium, Hot, Die with your Boots On, or Heaven Can't Wait).
Programmers love to do this. Examples include:
Soylent, a project to merge all contact info (e-mail addresses, IM screennames, etc.) for a person into a single account in GNOME (Linux-and-its-ilk desktop).
Plan 9 From Bell Labs, the successor to UNIX as Bell Labs' main research OS. Along with Plan 9 From User Space, a port of the main Plan 9 programs to UNIX-like systems. (and yes, userspace actually means something in context)
The TIFF standard specifies "An arbitrary but carefully chosen number (42)."
The ADA programming language, named after Ada Lovelace, who's often credited to be the world's first programmer. ADA was created under contract from the United States Department of Defense, which gave the ADA reference manual the number MIL-STD-1815. 1815 was Ada Lovelace's year of birth.
The Python programming language was named after Monty Python.
The term "Spam" for junk e-mail was named after the Monty Python sketch of the same name. Other people backronymed it to Stupid Pointless and Annoying Message.
While not a shout out to pop culture most of the time the codenames for AMD, Intel, and Microsoft products tend to be named after places they either do development in, take vacations to, or just because.
AMD's first in-house designed x86 compatible processor was called K5. Their next generation, K6, was when they said the K meant Kryptonite.
Since the Ge Force 200 series, NVIDIA's GPUs have been named after famous mathematicians and physicists. These have included Nikola Tesla, Enrico Fermi, Johannes Kepler, and, in an upcoming release, James Clerk Maxwell.
The Raspberry Pi (an educational- / hobbyist-market computing device with an ARM CPU, capable of running Acorn RISC OS) is available in "Model A" and "Model B" versions; this will sound familiar to anyone who remembers the BBC Micro. (It's no coincidence that this device was co-developed by David Braben, of Elite fame.)