Like most of the characters in Justice League International, Booster Gold underwent a fair bit of Flanderization in the title. He started off as a fairly likable, competent hero in his own book, but got progressively stupider and more vain once he joined the Justice League. It's even Lampshaded in Formerly Known as the Justice League, where Blue Beetle points out that Booster used to be fairly intelligent, and accuses him of acting dumb and childish on purpose. Later on, it is confirmed to be (mostly) an act.
Deadpool did not start off as stupid as he's famously depicted as being, and in fact was more of a standard mercenary in his first appearance in X-Force. The whole "Dumbest guy on the planet" personality didn't really come into effect until he got his own solo series.
Johnny Storm, AKA: The Human Torch, of the Fantastic Four, started out having at least average intelligence (a little cocky and reckless sometimes, obviously not a rocket scientist like his team leader, but not out and out stupid either), but as time went by and his characterization turned him more and more of a shallow, superficial, borderline selfish man-diva, Johnny became increasingly stupid to coincide with this more irresponsible characterization.
After Terry Moore took over Runaways, most of the cast had their intelligence downgraded in order to help make the series Lighter and Softer. It was particularly pronounced in Molly and Klara, who went from being unusually mature for pre-teens to being so dumb that they wasted a night trying to build a fort to defend against aliens with far better firepower.
Princess Leia in the comic adaptation of Star Wars novel Splinter of the Mind's Eye. In the novel itself she is a Shell-Shocked Veteran (leading to some Jerkass moments) but very smart and cosmopolitan. The comic cuts out a lot of these scenes leaving Luke to make essentially all the plans and guesswork, so Leia comes across as a little slow on the uptake.
Superman's IQ seems to drop a few points whenever he's with the Justice League, or more specifically whenever he's around Batman. Then again, Batman seems to have the power of making other characters dumber just by being there. Other times Superman gets dumber to varying degrees to contrast his super-scientist arch enemy Lex Luthor. And still other times, writers can't agree if Superman is a scientist like his father, how strong those scientific tendencies go, and how prominent his super-intelligence is.
In Superior Spider-Man, as a result of the Plot Armor of the protagonist, all the supporting cast of Spider-Man suffers from this. The worst example is definitely Mary Jane that, despite having lived (or married before OMD) with him and his alter-ego for a long time, she does not have the slightest suspicion that "Peter" is actually an impostor.