If you're up for a fairly strenuous hike with the payoff of fantastic views and a cozy English-style cottage waiting for you at the end, the Muir Beach loop along the Coastal Trail is a great choice. Muir Beach is a short drive from San Francisco, just across the Golden Gate Bridge and up into the winding hills of the Marin Headlands before heading down to Muir Beach itself. Muir Beach is smaller than the more popular Stinson Beach, and a bit more prone to fog, but it's still worth a dip (or at least a wade) if the weather cooperates.
Muir Beach — Photo courtesy of Wikipedia Commons
From the parking lot, take the Green Gulch Trail and follow the split to the beach where you'll find the Coastal Trail. The heavy climbing begins here, but the elevation gain offers fantastic views up and down the Pacific Coast. Give yourself three hours for this hike, allowing plenty of time to catch your breath and enjoy the views.
The loop consists of the Coastal Trail, Coyote Ridge Trail, and Middle Green Gulch Tail, which will lead you back to your starting point, as well as the big payoff for all your hard work: The Pelican Inn. As far as Marin after-hike watering holes, The Pelican Inn might be second only to the equally lovely Tourist Club. 
The Pelican inn — Photo courtesy of Tom Molanphy
If you've been blessed with a sunny day, grab a pitcher and your lunch and enjoy the weather on the Inn's front lawn. The menu is simple and just what you'd expect from an English-style tavern, with the excellent bangers and mash taking center stage. If the fog has rolled in, don't fret, because there's nothing better on a foggy day than a cozy English cottage with a fireplace, which is exactly what the Inn offers inside.
If you need something sharp and biting to snap the cold out of you, try the Pelican Inn's housebrew IPA, brewed locally by Lagunitas Brewing. Just the aroma of the strong hops is enough to break the dampness of the thickest Pacific fog. If that's not enough, go the traditional route of the hot toddy, and the warm whiskey will get your blood flowing to all the right places once again.
John Muir was legendary for his long walks. If you're up to the challenge, take a walk in his shoes for a day and enjoy the Muir Beach loop the next time you're in Marin County.