The "Phones-4-You" ad campaign goes from being a mildly successful attempt at Memetic Mutation to being pretty hilarious once you've played Metal Gear Solid 4, where the weapons merchant has a hand-gesture catchphrase for the slogan 'EYE HAVE YOU'.
It is generally quite hard to deliberately engineer a Hilarious in Hindsight moment, as it's all too easy to be offensive or to simply pander to an obvious in-joke. For a master class in doing it right, step forward the late, great British comedian Bob Monkhouse. Four years after his death in 2003, with thanks to modern digital wizardry, he appeared on television in an advert suggesting the wisdom of being tested for prostate cancer, cracking jokes about it being an even bigger killer of men 'than (his) wife's cooking!' so that the viewer doesn't end up 'as (he) did' - spoken while appearing standing beside his own actual tomb-stone.
At the time it aired, a McDonald's commercial featuring N'Sync and Britney Spears playing "spin the bottle" had a rather light-hearted punchline, whereby the bottle stops on Justin Timberlake, not Britney. A few years later, Lance Bass came out as gay, and it gives the ad a whole new meaning.
A drug PSA showed Pee-Wee Herman (Paul Reubens) talking about how dangerous crack was. Reubens would later go on to play a drug dealer in the movie Blow. Then again, he had already been in some Cheech and Chong movies, which are about drugs.
A 1996 This is SportsCenter ad featured Karl Ravech and Keith Olbermann interviewing former Senator Bill Bradley for a job. The last line of the commercial has them questioning whether he'd spoken in front of an audience. Bradley says he gave the keynote address at the Democratic National Convention. Olbermann replies, "We meant a large audience." One that a decade later he himself would try to tap.
T-Mobile made a series of anti-AT&T commercials, very closely modeled after Apple's infamous "I'm a Mac and I'm a PC" ads. Mere months later, T-Mobile was almost absorbed into AT&T.
Alltel Wireless also ran a series of ads spoofing their competition, with takeoffs of AT&T, Verizon, T-Mobile, and Sprint "employees" featured (and the Verizon character often the butt of the jokes) — until merger talks between Alltel and Verizon heated up. The Verizon character was quietly dropped late in the campaign — shortly before Alltel itself was dropped into Verizon.
Lebron James appeared in a State Farm commercial where he dreamed of playing for the Cleveland Browns. The team they were playing? The MIAMI Dolphins.
Also, one infamous Sega CD commercial has become this. "You still don't have a Sega CD? What are you waiting for, Nintendoto makeone?!" Nintendo was actually the last console maker to get into using CDs, with the Gamecube, and even then didn't use proper, full sized CDs until the Wii.
In a way, Nintendo had the last laugh on this one. They actually did attempt to contract with Sony to develop a CD-ROM add-on for the SNES. The deal went sour, resulting in Sony developing the device into a stand-alone console which went on to become a significant factor in Sega's exit from the console market altogether.
Back when Enron was viewed as a thriving corporation, they released a series of commercials with the theme "Ask Why?" Years later when Enron suddenly went Bankrupt shocking the country, the United States government asked them why? They got their answer when they discovered years of corporate fraud.
In some old Windows 95 commercials (such as this one here), Microsoft used a 2 by 2 grid of squares that were colored the same way as the Windows flag in order to demonstrate certain features, though it wasn't their official logo. 17 years later, Windows 8 shows up with a more tablet-oriented UI. Guess what their logo turns into?◊
The Brazilian arm of Fiat made an ad related to the 2013 Confederations Cup, entitled "Come to the Street", described as "the biggest bleacher of Brazil". Given that at the same time huge protests emerged in the country, the revolted people embraced it as an anthem. "Come to the Street" became their motto (along with "The Giant Awoke", taken from a Johnnie Walker ad) and was stamped and sung everywhere.