The most unusual hotel in California is definately the Madonna Inn
No two rooms are alike in this unique California landmark, famous for its waterfall bathrooms.
What’s Special About the Madonna Inn: One of the most wacky and tacky sites along Highway 101. The brainchild and passion of hotelier Alex Madonna, who died in April 2004, this 1950s monument to kitsch is easily recognizable by its Swiss-Alps-inspired exterior and Pepto-Bismol-pink color scheme. Tourists swarm to see the world-famous waterfall urinal. Each room in the Madonna Inn is uniquely themed; choose among rooms such as Old Mill, with a working waterwheel, or the Hearts and Flowers, where walls and floor are bright red.
Though it is in Central Coast California, but it is certainly worth checking out.
http://www.madonnainn.com/

Also check out:
Brookdale, California – Haunted Brookdale Lodge
Set under giant redwoods in the Santa Cruz Mountains, the Brookdale Lodge has a long history of entertaining celebrities, politicians and mobsters during the 1950s. Famous visitors include James Dean and Marilyn Monroe. One of the more unusual aspects of the lodge is the beautiful dining room with the natural brook running through it. Of course the reason why most people like to visit the lodge is for the rumors of ghosts. Witnesses have sworn to seeing the ghost of a little girl in a formal dress run through the lobby and then disappear into thin air. Other folks have claimed to hear strange voices in empty rooms – such as the Mermaid Room where you can spy on swimmers from an aquarium view of the pool.
831-338-6433
http://www.brookdalelodge.com/

Here are some more suggestions:
http://www.redvic.com/
Has some very unusual rooms. In San Fran.

http://jughandle.creek.org/
Also pretty unusual, and up north.

http://www.greentortoise.com/san-francisco-hostel/photogallery.php
Fun and unusual and in San Fran

And rather far away is:
http://www.wigwammotel.com/

There is this place in Los gatos that is cool the Los Gatos Villa Inn

or find a best western anywhere above San Rafael

http://oceanparkmotel.citysearch.com/

This was the first motel/motor lodge in San Fran. It’s Art Deco (built in 1936) and inexpensive. It’s one of those hidden places you’d never find in a tour book. It is near the ocean/SF zoo and they have kitchens in the room.

Enjoy your trip.