Pet-Friendly Hotel & Motels. Compiled by Carolyn S. on November 8, 2009

From my dog book "Dog Lover's Companion to California": 
Sheraton PA, dogs under 80 lbs. 650 328-2800 
Best Western Tropicana Lodge, Mt View 650 961-0220 
Residence Inn Mt View 650 940-1300 
Quality Inn, Santa Clara 408 241-3010 
Vagabond Inn, Santa Clara 408 241-0771 
Cypress Inn, Cupertino 408 253-8900 
It's a new dog book and so far, we have found everything in it reliable.

My sister stays at Residence Inn by Marriott® Mountain View Hotel 1854 El Camino Real West • Mountain View, California 
Phone: (650) 940-1300 with her dog(s) when she's in town. She's been very happy with the suites and the price.

I know that the Palo Alto Sheraton is pet friendly, but you can't leave the dog alone at any time, I think. Palo Alto is a very pet friendly town (more than anywhere we've ever lived). I do know that there are several places that do allow pets. Here's a website that lists other places. Feel free to pass it on to your friends... 

http://www.dogfriendly.com/server/travel/uscities/guides/w/cities/wonlinecityCAPalo_Alto_-_Peninsula.shtml

I just did a quick search with the terms "pet friendly hotel motel" 
and came up with this website : 
http://www.officialpethotels.com 
a quick search there shows 4 "pet friendly" hotels in Palo Alto and 2 in Mountain View.

I believe that Residence Inn accepts pets. They also have a mini-kitchen in their rooms. There are two in the Palo Alto/Los Altos area, fairly close to each other. The one on El Camino, next to where Elephant Pharmacy used to be (Palo Alto side of San Antonio) is nicer than the one closer to Mountain View. Hope this helps

The Cypress Hotel in Cupertino welcomes dogs. They do a nice job with them, and it is a great hotel. Might be a bit far from Palo Alto, but it gives you a start! 
http://www.thecypresshotel.com/

Jdvhotels.com. And kimptonhotels.com allow dogs

Motel 6's take dogs.