Over the course of The X-Files' run, Mulder was always on the hunt for the truth, and a series of shady informants helped him get closer to it. For Mulder, "The Truth Is Out There" wasn't just a catchy slogan on a poster in his office. Tormented by the mysterious childhood abduction of his sister Samantha, Mulder had made uncovering the truth behind the lies told to Americans every day his life's work. This most notably centered on the existence of aliens, and their dealings on Earth.
Mulder didn't just try to expose aliens to the light of day though. He also, along with partner Scully, investigated and proved to be real just every possible type of creature that's normally thought to be only myth and legend. Of course, the proof he was able to collect was rarely accepted by others, and was sometimes even stolen outright by the forces looking to maintain the cover-up. There's many reasons why the government and powerful people in smoke-filled backrooms don't want the public to know about such things.
In Mulder's corner on his quest for the truth were various men and women with knowledge of the conspiracy from the inside, but who had issues with how things were being implemented, or had come to regret their participation in it. These informants sometimes spoke in riddles, and would usually pick their own well being over Mulder's if pressed, but they still often provided valuable information.
Deep Throat (Jerry Hardin)
Played by prolific character actor Jerry Hardin, "Deep Throat" was Mulder's first informant on The X-Files, introduced in the second episode of the series. Named after an informant who helped break the Watergate case involving President Richard Nixon wide open, Deep Throat had a very friendly relationship with Mulder, and later interacted with Scully as well. He became a sort of pseudo father figure for Mulder, making it all the harder when he was gunned down in the season 1 finale after helping his protege out one time too many.
X (Steven Williams)
Played by Steven Williams, Mulder's next informant was known as simply "X," sometimes referred to as "Mr. X." He was named as such do to Mulder taping an X on his apartment window when wanting to communicate about something. Likely due to what happened to his predecessor, X was much more cautious about the information and help he provided to Mulder, and they had a sometimes contentious relationship. X too met a sad fate though, being shot to death by a Syndicate assassin in the season 4 premiere.
Senator Richard Matheson (Raymond J. Barry)
Introduced in season 2, Senator Richard Matheson (Raymond J. Barry) was a fan of Mulder's work on The X-Files, and used his power and influence as a politician to try and help Mulder's cause as best he could. That is until Mulder's goals and Matheson's goals started to butt heads, leading to a frosty relationship between the two. At least Matheson didn't end up dead.
Marita Covarrubias (Laurie Holden)
Mulder first encountered Marita Covarrubias, Special Representative to the Secretary General of the United Nations, in the season 4 premiere, not long after X's death. Covarrubias (played by future Walking Dead star Laurie Holden), like prior informants, does end up having close ties to the Syndicate, but she does seem to be helping him for good reasons. Of course, once the Cigarette-Smoking Man finds out, she's purposefully infected with the black oil, although she does survive the series, surprising as that may be.
Well-Manicured Man (John Neville)
Another mysterious character whose true backstory was never revealed, the Well-Manicured Man was a high-ranking Syndicate member that chose to aid Mulder for his own reasons. The Well-Manicured Man's final appearance came in the 1998 X-Files: Fight the Future movie, in which he informed Mulder of the Syndicate's plans for the coming alien colonization, before seemingly committing suicide via car bomb. It seems likely he did this to hide his treachery, and head off Syndicate revenge against his family.
Dr. Alvin Kurtzweil (Martin Landau)
The only Mulder informant to have never actually appeared in an episode of The X-Files, Fight the Future's Dr. Alvin Kurtzweil (Hollywood legend Martin Landau) knew William Mulder as a young man, eventually leading him to contact Fox with information from inside the Syndicate. Kurtzweil was immediately targeted by government forces, and naturally, his betrayal didn't go unpunished. The Well-Manicured Man killed Kurtzweil prior to his own death, dutifully carrying out his last Syndicate order.
Michael Kritschgau (John Finn)
An employee of the Department of Defense, Michael Kritschgau believed that Mulder was barking up the wrong tree, and that a conspiracy Mulder thought to be about aliens was instead merely a cover-up for secret military and government experiments performed on civilians. Kritschgau actually turned out to be wrong about the aliens, which he would learn after Mulder was adversely affected by an alien artifact. Kristschgau was subsequently taken out by Alex Krycek, one of the Syndicate's deadliest exterminators.
The Lone Gunmen (Tom Braidwood, Bruce Harwood & Dean Haglund)
The Lone Gunmen are an anomaly on this list, as they're not at all villainous, and aren't insiders in the government conspiracy. They most definitely are informants though, often using their intelligence and hacking skills to obtain useful information for Mulder and Scully. The group would of course go on to headline their own spinoff series, which lasted only a single 13-episode season, but did manage to spook everyone by seemingly predicting 9/11.
Susanne Modeski (Signy Coleman)
Susanne Modeski is in a bit of an odd category here as well, technically serving as an informant to Mulder's informants. Modeski worked with the army in the development of a powerful biological weapon, only to discover that her superiors planned to use this weapon on innocent people. Modeski formed a friendship with the Lone Gunmen, and also a romantic connection with Byers, as well as having memorable encounters with X-Files leads Mulder and Scully. Thankfully for her, she ended up receiving a new identity and escaping a messy death at the hands of the government conspirators.