We've taken our Cobra to two locations in Sonoma where I felt comfortable leaving her overnight (covered):
1. The Sonoma Mission Inn -
http://www.fairmont.com/sonoma/ - this is a very high end, luxury resort and spa. The offer vallet parking, however when we pulled in, the vallet lead us to underground parking that was very isolated from the "lowly" Benz's, Porsches, Bimmers, and such

While we were out during the day, the vallet kept "our spot" unoccupied by placing pile-ons in front of "our spot". I must admit that when I fired up our Cobra that early Saturday morning in the underground parking facility, it was kinda funny to watch (and hear) all of the car alarms going off
2. The Sonoma Valley Inn -
http://www.sonomavalleyinn.com/ - this is a Best Western located two blocks from "the square". We've stayed here many times, most notibly during the Nor Cal Mini-Nats. They have a separate parking area in the back in front of the suites. The maintenance man is into auto-cross, so he was more than happy to keep an eye on our Cobra.
Over New Year's we visited family staying at MacArthur Place (while we stayed at the Sonoma Valley Inn for 1/2 the price

. I agree with Cobradriver that it is a safe place - I would have no problem parking our Cobra over night there, as long as we were not staying in one of the "buildings" that face the main highway into downtown Sonoma.
Tho we've only taken our Cobra to Calistoga once, we've been there many times - most of the times we stayed at Dr. Wilkinson's -
http://www.drwilkinson.com/ . Calistoga is a nice cross between "Main Street" and a "sleepy little town". It's a place where you "park and walk". Besides Tom's advice for Indian Springs -
http://www.indianspringscalistoga.com/index.html - (which Bessie and I may try next month for anniversary), I highly recommend the Cottage Grove Inn -
http://www.cottagegrove.com/ - right across the street from the Indian Springs. These are individual cottages, beautifully decorated with reserved parking in front of each cottage - this is where we stayed when we drove our Cobra that one time.
Have Fun,
Randy R...