Museums of all kinds are wonderful, but big museums tend to be devoted to one conventional subject (like art or history-boring!), and feature well-curated, non-terrifying exhibits. This is why I prefer the type of museum that you stumble across by accident, the tiny dim rooms crammed with oddly incongruous artifacts. Here is a list of unconventional museums. I chose them mostly based on places I've lived; I'm sure there are hundreds of similar treasures I've never heard of. If you've been to a museum that deserves a spot on this list please let me know so I can add them to my imaginary road-trip itinerary!
The Musee Mecanique
San Francisco

Like many kids that grew up in the Bay, I was traumatized at an early age by Laughing Sal, a life-size doll who laughs hysterically and shakes with glee for an inordinately long time if you feed her a quarter. The Musee Mecanique is a treasure trove of old-timey mechanical creations that move and make noise for small change. As I recall, a lot of them tend towards the macabre, like a little diorama of a hanging or guillotining, but there are also cool matchstick circuses and arcade games. Nickelodeons give you a peek at sordid San Francisco history, including opium dens and Victorian ladies with exposed ankles.
The Wells Fargo Museum
San Francisco

I ducked inside this museum to escape the wind, even though it looks extremely boring from the outside. I sure learned my lesson, because Wells Fargo in fact has a thrilling history.

More importantly, you get to sit in a stagecoach, and there are exhibits like this display of gold labelled "Gold!" The Wells Fargo Museum is another great spot for fans of seedy, prostitute-filled, corrupt Barbary Coast history.
Kidd's Toy Museum
Portland, Oregon

I can't understand why tourists visit Portland; it's not a very flashy city, and there are few big attractions. Its true glory lies in places like Kidd's Toy Museum that even locals walk by for years without noticing. Housed in a nondescript, windowless warehouse, this museum is marked only by a small sign taped to the door that says "Toy Museum. If you knock and we open the door we're open." Inside is a maze of glass cases of antique toys, games, dolls, souvenirs, locks, and unexplained newspaper clippings. Apparently the collection of a rich guy named Kidd, the toys represent many sides of classic Americana, from advertising icons and circuses to really disturbing racist piggy banks.
The Velveteria
Portland

One of the few places on this list that purposefully caters to weirdos, the Velveteria is a delightful collection of that most vulgar style of painting, the bane of every hipster garage sale, black velvet painting. They have rotating shows devoted to classic subjects, like Elvis, matadors, and of course, babes with afros. Don't miss the blacklight room.
Pollock's Toy Museum
London

This adorable little dollhouse of a building is the good twin to Kidd's evil. It specializes in theatrical toys: puppet theaters, elaborately costumed dolls, and quaint European folk dolls. When I went there they were on the verge of going bankrupt, but according to the website they're still around. Thank God!
Museu de la Xocolata
Barcelona

Food museums are big in Spain: there's also ham museum in Madrid. Barcelona's not really known for it's chocolate, but that's just the beginning of the museum's weirdness. Unflattering chocolate likeness of Ronaldinho and Messi greet you at the entrance, and inside there are dusty chocolate sculptures of Willy Wonka's factory, Don Quixote, Salvador Dali, every famous building in Barcelona, and a full size Pieta. I pressed a button next to a movie projector, expecting a nice video about how chocolate is made, but instead it was a horrific, acid-flashback-inducing montage of Aztec gods, creepy stretched out faces, conquistadors, and blurry landscapes (set to a soundtrack of clicking and roaring noises).
Proteus Gowanus
Brooklyn

Housed in a warehouse near the intriguing, awful-smelling Gowanus Canal, this little space has all the makings a great museum: books of dubious truthfulness, taxidermied animals in drawers, and lovely art. Proteus Gowanus includes reading rooms devoted to anatomical aberrations and local history, and a gallery with a particular theme every year. It's a modern wunderkammer as well as a thriving community center.
The Museum of Jurassic Technology
Los Angeles

I put off writing about this museum until the end because I still can't think of how to convey it's brilliance and humor. The Museum of Jurassic Technology is all I've ever dreamed of concealed behind a storefront in Culver City. Miniature popes made of hair, bats that fly through solid walls, Russian astronaut dogs, women with horns, and forgotten philosophers populate this enchanted space. The museum's creator, David Wilson, won a MacArthur Genius Award, and is the subject of the book Mr. Wilson's Cabinet of Wonder, by Lawrence Weschler. I recommend reading it, but mere words cannot capture the MJT, though they are a part of its web of half-truths. Even during the Great Recession, a visit to the Museum of Jurassic Technology is worth the price of a flight to L.A. and the five dollars suggested donation (though your inevitable affection for Mr. Wilson and Co. will compel you to donate more). Even writing this makes me want to move back to California to be closer to it.