Sacramento, like San Francisco, was a city born of the 1849 Gold Rush. Located along the primary river route, it served as a lifeline for supplies to the gold fields of the Sierra Nevada. The original waterfront of the town, part of which has been preserved as the Old Town Sacramento district, does not sit at ground level. Floods from the Sacramento River damaged the goods and properties of the people working and living in this area, prompting them to construct an upper level to which most businesses and homes were moved. To the casual observer, the upper level appeared to be the ground level.
The lower level did not vanish, however, it simply became invisible to those who lacked access to the tunnels via the former-first floors (now basements) and various tunnel entrances. While the tunnels were likely used for numerous legitimate activities (storage, lodging, etc.), they likely also served the (now literally) underground economy as a home to prostitution and opium dens. The tunnels are no longer readily accessible - you have to have access to a property with a connecting basement to get into them - but are still there and can be entered by those who know a way in (mostly owners of buildings with connecting basements, although some other folks find access as well). Much like similar tunnels in Portland, Oregon, these tunnels eventually gained a reputation for being the dwellings of unnatural horrors.
Rumors abound of strange lights and unexplained shadows in the tunnels. Property owners (and those who work in the area) with access to the tunnels are rumored to report a strong sense of malice directed at them when they enter the tunnels. One rumor holds that even transients won't sleep in the tunnels due to constant feelings of being threatened by some unseen force.
Although there are likely more specific hauntings known for the area, these are hard to find through research. It's the ambiguous lighting and feelings of menace that one finds mention of when looking for information on the tunnels.
Commentary: Abandoned places attract ghost stories like Paulie Shore attracts loathing, and a place that is not only abandoned, but hidden? Well, that's a recipe for stories of hauntings. So, the fact that the subterranean portion of Old Sacramento is reputed to be haunted is not surprising.
What is surprising is how little information is in any way specific. While I have no doubt that had I the time to go and interview people who have spent time in the tunnels I would have heard at least a few specific stories (a particular location where lights are seen, a ghostly voice that calls out, an apparition of a person or animal, etc.), in trying to research this remotely online, all I can find are rumors, references to vague feelings of dread or evil, and announcements that some people refuse to enter the tunnels.
It's a bit anti-climactic.
So, in the end, the idea of a town buried under your feet is a bit creepy to begin with, and the fact that this town is reputed to be haunted amps up the spookiness level. But if you look too deep, you tend to find no meat to sink your story-collecting teeth into. It's frustrating.
Oh well, at least it's still a cool location.
Extra Stuff: A series of photos of exposed underground locations can be found here.
Sources: Internet, Internet, The Illustrious Internet, Internet