Background: I've started documenting some of my favorite medium-difficulty and advanced-difficulty runs in the San Francisco bay area. The advanced runs are for extreme runners who are masochistic, at best. You can find out more about me here.
WARNING:These guidelines are ideas for difficult runs; runners must use their own judgement when attempting any strenuous run. ***These runs should not be attempted by non-expert runners.*** Many of these routes travel through sparsely populated regions; I strongly encourage buddies so that if problems happen, someone can get help. If you insist on running alone, make sure someone is expecting you to check in afterwards so that they can send help in the event that something happens.
Stanford Foothills & Felt Lake environs (the area bordered by Junipero Serra Boulevard, and Arastradero and Alpine Roads)
This set of running locations can entertain runs that are as challenging as you wish to make; you can lengthen runs in interesting ways. It is ultimately a set of extensions for and around the Stanford foothills. Much of the terrain is out in the sun in rolling hills. Depending on your choice of routes, you may have a large amount of pavement. Please note that this region covers property with varied ownership and access restrictions which may change. I'm not going to try to reflect those various restrictions here, but I advise looking out for them and observing them with care.
Directions: Drive to Stanford, basically. Take 101 to PageMill/Oregon Expressway, Right on El Camino, Left on Stanford avenue. Drive until you Stanford Avenue ends and you see everyone parking...park with them at Junipero Serra, near the entrance to the foothills.
There are several starting routes. One is to skirt the edge of the Stanford foothills along Old Page Mill Road, eventually under the freeway, and right onto Arastradero Road, leading to the Arastradero preserve (see below). You can skirt the preserve, past the Felt Lake area to the right, and past the preserve on the left. Felt Lake is fairly hidden, with a set of dirt trails surrounding the lake several miles in length. You can identify it on satellite maps (try maps.google.com, pointed at Stanford, and look for the lake just south of I280). Arastradero road eventually runs into Alpine road, which you can follow right on the paths back towards Stanford. Alpine Road eventually leads you back to Junipero Serra boulevard, which you can turn right on and follow back towards the foothills and your vehicle. Along the way, there are often side trails and soft surfaces you can choose to run on.
Alternately, you can include the Stanford foothills in these runs. There are several public access points, two along Junipero Serra, and one leading down the back side near Alpine road and interstate 280. Back where you parked your car, you can run up the paved trail leading towards the top of the foothills, crest the hill, and then descend rollingly towards a valley between peaks; the other peak has the big satellite dish on it. After the satellite dish is where the trail leading out the back side to Alpine road takes off to the left. Continuing straight leads to the other exit on Junipero Serra. There are other trails in the foothills, including one in between the two peaks near the satellite dishes that leads down the backside of the hills and under highway 280 through a tunnel with cattle grates to Felt Lake, but it was fenced off when last checked.
The Arastradeo Preserve and Foothills Park
The Preserve isn't very well known, so you won't find references to it elsewhere, although it is on maps.
Directions: Take Hwy 101 to Page Mill/Oregon Expy, then take Page Mill all the way under I-280 (about 10 minutes). Once you go under I-280, the road curves a bit, then you come to a stop sign. Make a right (the road is Arastradero), and drive until you see rolling hills with grass and trees -- there is a parking lot on the right which stays open until dusk.
Take the main trail (mostly gravel and dirt) which winds up through a valley and along a few very quiet ponds. There is a fork by a power station; go left, up two more hills, and past some additional ponds. You'll run up a slow grade for about half a mile, and then you'll come to a sizeable hill. Run up it. When you reach the top, go down the hill to the gate, and into Palo Alto's Foothills Park. Take the dirt trail to the right. Follow it all the way to its end, which is a road. Go left on the road to its end, past the park headquarters and onto a dirt access road. Watch for a bridge on your left. Take the bridge, run up the ridge. At some point, you'll pass a trail intersection, but stay straight and keep going up. After reaching the top, continue onwards, until you reach the next trail taking off to your left. Take it down to the road again, and follow the road up to the lake. At the lake, take the trailhead on the left, around some ridges, and then make a right turn at the first intersection (after crossing a plank bridge). At the top, head left down the road (or stop to admire the view). Then look for some piles of brush blocking an old trail going over the side of the hill. Go around them, find the trail, and proceed down to the fence which marked the entrance to the park. Alternately, take the road down to the gate you came through earlier (note: if the road you take goes to the lake, you're going the wrong way. Then run all the way back to the parking lot down the nice, long downhill. (PS: stretch your quads and calf muscles a *lot*)
This run starts at around 8 miles, and can be extended in the various ridges around Foothills Park and Arastradero Preserve. On hot days, it can get intense.
Huddart Park, Phfleger Estate, Lonely Trail, Skyline Trail, and Wunderlich Park
Here we go kids: 1700 feet of elevation gain, but you do it the hard way. There are many variations here, but I'm going to give four variations: 10 miles (Dean Trail), 12 miles (Phfleger), 14 miles (Phfleger + Lonely) and 20+ miles (Huddart to Skyline to Wunderlich). These are some of the best trails in the bay; deep in forests and steep in hills, they are great for staying cool on hot summer days.
I usually park near the Woodside Store, so I do not have to pay to get into the park. Alternately, you can add an extra 2 miles to your run by starting at Woodside Elementary School, and running down Woodside Road to King's Mountain Road. Take Woodside Road through Woodside the town, until you hit Kings Mountain Road on the right. There is a sign for Huddart Park. If you drive over a bridge, you've gone too far. Take Kings Mountain Road past some big estates, and find Tripp road on the left with a historic monument (the Woodside Store). Park along Tripp road near the store (they close the gates at ~4pm).
Run along Greer road into Huddart park; there is a dirt path along it leading to the park's back entrance. Once you enter the park at the horse gate, find the only dirt trail, and cross the long footbridge. The trail winds up a hill a bit, until you come to a field with a bathroom. The trail that takes off at the gate is Richards Road which you can run on for a long ways.
Route 1: 10 miles. At the horse gate, there is a second trail called the Bay Trail which immediately heads up and to the left. Take it, all the way until it emerges into a clearing some miles ahead. Continue straight until you come to the start of Dean Trail on your left. Take Dean Trail up and over many switchbacks, exiting any populated part of the park and over some rolling ridges until you emerge onto McGarvey Flat. Continue onward (usually after pausing to admire the scenery) until you reach Crystal Spring Trail. Take Crystal Spring down a long way until you reach Richards Road. Take it downwards a long way until you get back where you started.
Route 2: 12, 14 and 20+ miles. At the horse gate, take Richard's Road all the way until it makes a 160 degree turn, which you should go around and follow until you take a trail off to the right which heads downward to the river valley and into the Golden Gate National Recreation Area / Phfleger Estate. Take that trail a good few miles; you'll wind along a creek, and eventually make a sharp, left turn up the ridge to the left. The ridge flattens out and emerges into a trail intersection. Continue upwards. This is a very challenging mile long hill (maybe longer). Eventually, you'll cross the valley at its end, and continue up the other side to another trail intersection.
Here, you'll see Lonely Trail take off to your left. For the 12 mile loop, ignore it, head the other direction back down into the Phfleger Estate and the San Andreas Rift Valley, and you'll eventually cross a bridge and be back in the previous intersection, from which you can retrace your earlier route.
For the 14 and 20+ mile loops, take Lonely Trail. This is another good mile or two of climbing up to the top of Skyline Ridge. When you eventually emerge at the top, you can choose to follow either Richards Road or Crystal Spring trails back downwards for the 14 mile loop. I suggest Crystal Spring, but it can be trickier to find. These are *long* downhills, so don't overdo it.
For the 20+ mile loop, find the SkyLine trail and run along it to the south (generally speaking, left or straight). 7+ miles later, after several moments of potential confusion near several houses, you'll see trails taking off down the mountain for Wunderlich park. don't miss this trail -- I don't know where the next "down" trail is, and I doubt you want to explore to find it! Take any and all trails leading downward through Wunderlich park. Keep going down and you can't get lost. Eventually, you'll emerge in the parking lot, and you'll want to follow Woodside Road for several miles all the way back to either Kings Mountain Road / Tripp Road and your car, or all the way to the elementary school.
Warning: This 20+ mile loop should only be attempted by extreme runners who know they are capable of it. It involves significant, challenging mountain running, followed by near-marathon length stretches running through areas devoid of human travel (and hence help). Hydrate beforehand, carry a small survival pack against exposure to the elements, as well as a small phone, and pace yourself carefully. Even if you do runs of these lengths regularly, doing them away from people carries higher risk because the consequences of injury or mishap are more severe.
I recommend carrying a detailed map of the area before attempting these runs; at a minimum, either study or carry a map of Huddart and Wunderlich parks. (found on the San Mateo park website below); they also have them sometimes near park entrances.
To be added when I get time to run it again and document it...
If you're up for the drive north of the golden gate bridge, this is one of the best hill runs to be done in the area. There are hikers, but still take some minimal stuff with you to keep yourself hydrated and also warm, as the top of these hills can get foggy. Anyone familiar with the Dipsea trail, myself included, will recommend that you do it your first time with a partner, preferably someone who has done it before. Some of the trails aren't well marked, so it could be a bit of an adventure otherwise.
There's better documentation other places online, so I won't go into the route in too much detail here, but basically you park at Old Mill Park in Mill Valley, and look for the trailhead heading up into the hills. Lots of switchbacks, hill climbing, etc eventually get you up and over the hill and back down by Stinson Beach (you'll emerge fairly near to the firestation). It's 7.1 miles each way, and roughly 2000 feet each time you go up and over.
This isn't really the Bay Area, I know, but kinda an adjunct, at least in my mind. Anyhow, this is obvious mountain country, with all the risks it entails (which is to say, *lots*. Take survival gear: emergency blanket, water, iodine pills, radio/phone, and make sure someone knows where you are and when to expect you to check in).
I enter Desolation at one of two points: either Emerald Bay, or Fallen Leaf Lake. From Fallen Leaf, you can do a great run up and over Tallac and back down the side (12 miles), or add on the extension around Fallen Leaf lake (6 miles) -- note that you can do a flat run just around FLL -- or up through Dicks Pass and out at Emerald Lake (My guess is this is close to 15-20 miles depending on your route). For flatter runs, get dropped off at Echo Lake, running in while already at elevation, and then exit at Fallen Leaf Lake.