National Treasure/WMG

The City of Gold was built by a Goa'uld.
Let's face it: it's the kind of ridiculously self-indulgent project a Goa'uld would have come up with, and the quasi-Mayan design fits the Goa'uld well. This also explains why The Government tried to cover it up. (hey, there might've been a Stargate in that city!)

Thomas Gates was in on Lincoln's assassination.
The gang doesn't find any evidence which disproves this. And Ben is awfully smug about how great grand ol' Tommy was. Therefore, he's mistaken.

The whole series is in Riley's head.
Riley is a mental patient, and everything is his delusion. This is evidenced by the fact that Riley is the only character to ever say or suggest, albeit usually sarcastically, anything which makes sense. Whenever he falls into being as nonsensical as the others, he's succumbing to the delusion.
 * Riley's actor Justin Bartha portrayed a mental patient in Gigli.

The third film will be about the Fountain of Youth.
It's a "life-altering" discovery, to be sure; it's one of the few Americas-based discoveries we would have left to make; and most of all, it could lead into a cute little cross-over with Pirates of the Caribbean if Ben & Co. discovered Jack Sparrow had discovered it before them and just used it to keep himself young for hundreds of years.
 * Of course, this also ties in with The Last Crusade as Henry Jones Sr. used his already-extended life to find the Fountain as well, and his elderly son and grandson go off to find it with Ben.

The third film will be about the search for a massive bronze lumberjack with his gigantic sapphire ox.
Pretty much self-explanatory.

The third film with be about the lost city of Atlantis.
One of the most popular theories about the next adventure, assuming they can find ways to weave clues through out American history on top of everything else going back to Plato's days.

National Treasure 4 trailer quotes:
"You think that the Earth's core.... is made out of solid gold?"

"You're saying that George Washington.... is still alive?"

"We're just straight-up going to the Moon."

""I'm gonna have sex with the Declaration of Independence""

The third film will feature a WWI/WWII conspiracy.
First film had the American Revolution, Second film had the Civil War, so the third film should have a conspiracy from a later time period. Naturally the two world wars are prime candidates. Perhaps the real reason America intervened in WWI or the real reason behind Pearl Harbor. Or maybe the Kaiser or Hitler were trying to concur their way to a treasure containing the key to world domination?
 * If they do that, I really hope they do the WWI route, not the WWII one because We've got enough of Hitler and the Nazis in our movies.
 * Plus, Indiana Jones has covered WWII conspiracy stuff pretty well. For Ben to do it would seem redundant.
 * Isn't there an urban legend/conspiracy theory about Nazi Gold?

The third film will involve the supposed alien crash at Roswell, New Mexico.
Page 47 of the Book of Secrets detailed the US government's search for secret alien gold. The President has employed Ben to find it.