I've stayed at the Holiday Inn Express in Marin County. It's a pretty standard roadside hotel. It's not within walking distance of either Sausalito or Mill Valley. But is handy to the highway. If you plan on spending some time exploring Marin County (Stinson Beach, Pt. Reyes, Tomales Bay, Sausalito, Mill Valley, etc.) by car it wouldn't be a bad base of operation. However, if you only plan on visiting Muir Woods and then returnng back to San Francisco that is a simple enough trip from San Francisco itself. Starting at the Holiday Inn Express in Marin County would save you about a half an hour versus starting in San Francisco.

John in San Diego