Does anyone have recommendations on where to stay in San Fran and what to do besides the obvious also good places to eat. Thinking of going in Oct. Thank you in advance.

Not sure what weekend you're looking at, but be forewarned that October 18-19 will be especially busy for hotels, as that's the Nike Women's Half Marathon Weekend; lots of out-of-town runners in San Francisco for that race

Thank you , will defiantly stay away then.

I work as an Admin Asst and I book a lot of travel for my team. SF is not generally low-cost for hotels, but they like:
-Four Season SF
-Westin St. Francis
-Intercontinental Mark Hopkins
-Fairmont San Francisco

I was able to find a great rate last September on Hotwire for the Hotel California near Union Square. Came with breakfast and the room was clean and because of tradition a tequila shot at check in (which was super fun at 9am). Just looking at the site, it seems like they no longer have breakfast...

Am Bains
Cafe de Lucchi and Mama's for breakfast. Delicious!! In North Beach /Little Italy

Following.. I'm planning, hopefully next year.

Sigrid I was thinking of the Fairmont

Great Tiki bar, The Tonga Room

I enjoyed staying by the wharf and stayed at the hyatt and the hilton. So many things nearby within walking distance.

The Clift Hotel is great! The Little Chihuhua has the best burritos in town too!

I would second Mama's for Breakfast, it's out a ways but you can take a bus. Great food! The Wharf is fun and Union Square has great shopping. Alcatraz tour was one of the best I've been on and I travel a lot! There are great Boutique Hotels that are quite different. I stayed in the Executive Hotel Vintage Court. This was several years ago mind you. The lobby and rooms are great. The hallways were dark, vintage I felt like I was in a old movie, similar to the Shining! LOL