It's important to note that the Marvel guys have given subtle nods that they know about the connotations of the name. Actions have been taken by some members, most often chiefly Iron Man, in certain storylines such as the three listed above, which were not only disagreed with by at least one fellow member on principle, but also would call into question for readers whether they were playing this trope straight. Also, Iron Man says once to Maria Hill when remarking on this group and referring to it by name that “at least that’s what I self-deprecatingly call our little world-saving group,” giving clear hint that only he uses the name. Put this in perspective. The only member of the "good guy Illuminati" that ever used the name was the snarky/humorous member of the team who's led questionable acts in the plots that developed after each of its meetings, and even he readily admits it's self-deprecating humor.
Also notable to say that Black Panther refused the invitation to join because he knew that the group's extremely secretive nature left them doomed to fail if they ever disagreed on anything.
In DC Comics, the Illuminati hails from as far back as the days of Atlantis, has a covert hand in government affairs worldwide, and has been led by Vandal Savage from its birth to the modern day.
Mentioned in From Hell, along with a number of other secret societies, though the Masons take center stage.
Duumvirate is written from the point of view of the Illuminati themselves.
Robert Shea and Robert Anton Wilson's Illuminatus! trilogy helped spread the name. The books are a Mind Screw told by Unreliable Narrators and infamous for giving complex explanations for the origins of the Illuminati, and then subverting them later on, sometimes with information that is equally wrong. It doesn't help that there have been several groups throughout history under that name. The original Illuminati, according to the book, are Atlanteans who have been hiding under the Himalayas. Also there is a gigantic pyramid-squid.
Dan Brown uses the name in his various books, most prominently, in Angels and Demons. Here, the Illuminati are a secret society of scientists founded by Galileo Galilei to spread the Enlightenment (hence the name) and to oppose the reactionist Roman Catholic Church. Although they are thought to have been destroyed long ago, Langdon is drawn into a plot aiming to blow up the Vatican City, which he believes is the Illuminati's revenge. It turns out, the Illuminati really ceased to exist and the whole crisis was orchestrated by a traitorous Church official (who had access to the seized Illuminati artifacts) to bring himself into power, and restore faith in Christianity to the world.
TNA's latest Power Stable Immortal played this mostly straight at first, from the mass of foreshadowing to the ominous date of their takeover to the things they said to the quality of their regime's first show. The one subverting element was their "Ancient Conspiracy" is only ancient compared to the lifetime of most plots in wrestling. But then Fortune rebelled and Jeff Hardy tanked a pay-per-view. Immortal still remained, but their illusion of ominous power plummeted and would only continue to fade since.
And of course the nWo who pretty much ran WCW for the better part of four years both in storyline and behind the scenes.
Steve Jackson Games sells various conspiracy-themed card-games (collectable and otherwise) under the blanket name Illuminati, while their line of GURPS role-playing material have published a couple of Illuminati-related source-books. Some of it is obviously inspired by the Illuminatus! book trilogy. The company has a trademark on a least one version of the "Eye in the Pyramid" design, and the other companies in this section often get official permission to use it. Particularly WMG-worthy is the fact that several world-changing events in recent history seem to have been depicted on these cards in these games years before they happened.
Deus Ex. And they're debatably the good guys. Their rogue spin-off organization, the Majestic 12, on the other hand, are decidedly not.
Also featured in the prequel Human Revolution. Taggart describes the Illuminati as "just a name used to get rich people to invest more money," and he's not far off; the organization's every attempt to assert more control over the world goes completely off the rails, often due to internal sabotage. It's no wonder the first game's Big Bad was able to usurp nearly all of their resources for Majestic 12. Of course, Taggart is a lying liar who lies, and the organization was able to transform Zhao and Taggart from small fry to global power brokers.
The Illuminati is one of the three playable factions in the conspiracy-themed MMORPG The Secret World, along with the Templars (who are not, but have ties to, the historical Knights Templar) and an Asian-themed "Dragon" society.
Street Fighter III's antagonist leads an interesting take on this. The Illuminati in these games have a lot of religious symbolism and are more akin to a psychotic cult than an oppressive secret society. Gill himself is a Nietzsche Wannabe dark savior with obscene doses of A God Am I. Oh, and then there's the fact that he's red and blue skinned and clad in a thong... Although, they do have the whole Ancient Conspiracy thing going on.
Metalocalypse has the Church of the Black Klok, an ancient religious group that has foreseen all of the events surrounding Dethklok, brought Ofdensen back to life, and guarded the prophecy that details how Dethklok will save the world from the apocalypse brought on by Salacia/The Half Man.
One episode of American Dad! features a group called the Illuminuti, which guards the secret history of peanut butter.
In Young Justice, The Light seems to have a lot of Illuminati-characteristics, down to the name ("The Light" being very similar to "the enlightened ones"). In addition, the first member of The Light is Vandal Savage, who formed the Illuminati in the comics.
As noted above, there is some historical basis for the Illuminati. During 1776, a group of Bavarian Germans formed a secret society and used "Illuminati" as their name. The self-imposed mission of the Illuminati was to fight against abuses of state power, superstition, religion, and prejudice. The organization did get pretty popular, having members from many other parts of Germany, and earning the hatred of the Catholic Church. However, it was banned by the Bavarian government and disbanded in 1785. According to the conspiracy theories, this was just the beginning: The Illuminati actually left Bavaria for Scotland, infiltrated the Masons, founded America, and now control the entire world from a smoke-filled room. This includes TV Tropes.
If you're wondering how the historical Illuminati achieved such a prominent place in conspiracy lore, it's largely because the Illuminati's disbandment was followed shortly by The French Revolution. As the French revolutionaries had espoused the same Enlightenment ideals as the Illuminati, it was easy for the more paranoid European rightists to hallucinate that the French Revolution had been orchestrated by a still existent Illuminati. After that, it was on. Throughout the nineteenth century, politically reactionary circles blamed every leftist movement and revolution on Illuminati subversion. Make no mistake, the Illuminati conspiracy theory was started by religious monarchists who thought secular democracy was the most evil thing ever. The Illuminati theory was taken up by fascists in the early twentieth century and by the John Birch Society during the Cold War. At this point, the theory had clearly lost touch with its roots. Whatever else can be said about the John Birch Society, they're definitely not monarchists. Indeed, the John Birch Society changed the Illuminati from proponents of secular democracy to proponents of Soviet-style communism. Perhaps it's not surprisingly that subsequent mutation would change it from being an exclusively right-wing conspiracy theory to the apolitical one it seems to be now. In the current version of the conspiracy theory, the Illuminati is apparently in favor of some kind of generic totalitarian state, practically the opposite of what the real Illuminati wanted.