I was always partial to
The Very Big Corporation of America - VBCA and
The Crimson Permanent Assurance - CPA of course 
from Monty Python’s The Meaning of Life.
Although they are races of sorts-- The Tleilaxu from Dune and Kaminoans from Star Wars are biomedical and cloning monopolies. I don’t know if they are represented by specific holding companies or if it’s just more of a cultural industry.
There is also Quitters Inc. from the self-titled Stephen King short story. The story is from the book Night shift and adapted in the movie, Cat’s Eye.
General Services, from the Heinlein story “We Also Walk Dogs” – GNSR
The 19th Century inventors Frank Reade and Frank Reade, Jr. (http://www.bigredhair.com/frankreade/index.html), had an electronics/inventions business in Readestowne, NY, but I don’t know if it was ever named or incorporated.
CC : The Crimson Corporation from Star Control 2. Love those guys.
Aero-Tech from Space - Above and Beyond
General Forge and Foundry - GFF
From Vonnegut’s Player Piano (kinda sci-fi) and others.
Extensive Enterprises–the front corporation for the terrorist organization Cobra, from G.I.Joe.
All executives in the firm are actually members of Cobra’s elite Crimson Guard (LINK)
Isn’t their stock symbol GE? 
Ghostbusters, Inc.
And yet you ignore Acme???
Don’t forget Renraku (RRK), Ares Macrotechnology (AMT), Lone Star (probably a private company), Shiawase (SWA), and Aztechnology (RAZA).
Strictly spreaking, it’s not really “fictional.”
Anyway…
•Benthic Petroleum—The Abyss; Terminator 2 (BPET)
•Rossums Universal Robots—R.U.R. (RUR)
•Seburo—Many of Masamune Shirow’s anime and manga works. (SBRU)
•WcDonald’s—any number of animated works, anime or otherwise. (WCD)
Solar Spice & Liquors (Poul Anderson’s Van Rijn/Falkayn stories)
Post Terran Mining Corporation (from the Descent game series) – PTMC
Does World of Warcraft count? There’s the Venture Mining Company. Buncha damn goblins…
For an obscure one, how about “Con-Amalgamate.”—from Capricorn One and Outland. (COAM)
Nice work adding stuff in from comics. Wayne Enterprises was a good suggestion. I tried to remember anything that might have played a role in the X-Men, but I’m drawing a blank. The closest that I could get was Oscorp from Spiderman, already mentioned here from the Marvel universe.
Inspired by Scupper’s link, I dug up my copy of Snow Crash. Lotsa companies in there:
The Black Sun - BKS
CosaNostra Pizza/The Mafia/The Our Thing Foundation - OTF
Radical Kourier Service (RadiKS) - RDK
Pearlgate Associates - PLG
Central Intelligence Corporation - CIC
Mr. Lee’s Greater Hong Kong - LHK
These among what must be dozens.
Also, apologies if this has been mentioned, but I forgot Kuat Drive Yards from Star Wars. Lesse… KDY?
From Doctor Who:
Galactic Salvage – GAL (“Galactic Salvage went out of business years ago.” “They did? I wondered why I hadn’t been paid recently.”)
The Company – CO (from “The Sunmakers”)
In other Gibson series:
Sandbenders (SBN) and SlitScan (SLS) from Idoru
How could I have forgot earlier? The Frobotz corporation (FRBZ), openly traded in all of the stock exchanges in the Underground Zork Empire.