I love dogs, but sometimes wish their owners would go to obediance school. I have had dogs run after me, bark and growl at me, jump up on me, nearly knock me over, and any combination of the above, on trails. 

Here are some preserves and/or trails to avoid if you'd rather not tangle with the dogs:
• Pulgas Ridge Open Space Preserve, MROSD, San Mateo County
• Fort Funston, GGNRA/NPS, San Francisco County

The following trails/preserves don't allow dogs:
Marin County:
• Angel Island, CSP
• China Camp State Park, CSP
Dogs allowed only in developed areas. Dogs not allowed in the following areas: trails, dirt roads, backcountry areas, historic buildings, and historic gardens. • Marin Headlands, GGNRA (dogs permitted on some trails -- check website for details)
Owl Trail
Hawk Hill
Muir Beach
Dogs are permitted on Muir Beach and on some Headlands trails (they are not allowed on the trails featured on this hike)
Point Bonita
Rodeo Beach South
Slacker Hill
Tennessee Valley Trailhead (only permitted, leashed, on Oakwood Valley, Orchard, and Alta trails). Tennessee Valley is one of the most popular hiking destinations in the Bay Area.
• Martin Griffith Preserve/Audubon Canyon
• Mount Tamalpais State Park, CSP
Pantoll
Matt Davis-Steep Ravine loop
• Muir Woods National Monument, NPS
• Muir Woods from Mountain Home trailhead
• Muir Woods-Coastal Trail loop
• Olompali State Historic Park, CSP
• Point Reyes National Seashore, PRNS (no dogs on any trail except Kehoe Beach Trail; check the Point Reyes website for more beach info)
Abbotts Lagoon
Bear Valley
Chimney Rock
Estero
Five Brooks
Laguna
Lighthouse
Marshall Beach
Muddy Hollow
Palomarin
Sky
Tomales Point
• Barnabe Peak, Samuel P. Taylor State Park, Devil's Gulch area, Samuel P. Taylor State Park, and Pioneer Tree Trail, Samuel P. Taylor State Park Dogs must be on leash at all times and are allowed only in the following areas: day-use Picnic Areas; campsites (excluding the Hike & Bike campsite and the cabin area); on the Cross Marin Trail Bike Path. Dogs are not allowed in the following areas: trails (except the Cross Marin Trail Bike Path); Hike & Bike Campsite(s); Madrone Cabins; creeks; any other undeveloped areas or open spaces.
• Santa Margarita Open Space Preserve, Marin County Open Space
• Tomales Bay State Park, CSP

Napa County:
• Bothe-Napa Valley State Park, CSP (dogs are not permitted on trails, but they are allowed in the campground)
• Moore Creek Park, Napa County Open Space District (Dogs are allowed on the Lake Hennessy Unit only and must be on leash at all times. Lake Hennessy is the key source of drinking water for the City of Napa – no contact with water is allowed at any time. This includes swimming, dogs, horses, or any other animal under your supervision. Dogs are not permitted on the hike described in the link.) • Napa River Ecological Reserve, California Department of Fish and Game (no dogs). Just northeast of Yountville, Napa River is a fun stop if you're in the area. Trails are flat and lush (sometimes overgrown) in summer.
• Robert Louis Stevenson State Park, CSP (dogs are not allowed on trails).
• Skyline Wilderness (dogs are not allowed on trails).

Sonoma County:
• Armstrong Redwoods State Natural Reserve, CSP (dogs are not allowed on trails, but they are permitted on paved park roads).
• Austin Creek State Recreation Area, CSP (dogs are not allowed on trails, but they are permitted on paved park roads).
• Bodega Head Trail, CSP (no dogs on trails).
• Jack London State Park, CSP. Dogs are only allowed in designated historic areas including the Beauty Ranch area and on the trail to Wolf House Ruins -- they are not permitted on any other trail.
• North Sonoma Mountain, SCRP (no dogs on trails).
• Shiloh Ranch Regional Park, SCRP (no dogs on trails, but they are permitted in the picnic area). Lots of variety at this park north of Santa Rosa.
• Kortum Trail, CSP (no dogs on this trail, but they are permitted on some nearby Sonoma Coast State beaches).
• Sonoma Overlook Trail (no dogs on this trail).
• Sugarloaf State Park, CSP (no dogs on trails, but they are permitted in developed areas).
• Trione/Annadel State Park, CSP (dogs are not allowed on trails, but they are permitted on paved park roads).
• Tubbs Island, San Pablo Bay National Wildlife Refuge, U.S. Fish and Wildlife Service (dogs are only permitted accompanying hunters during hunting season).

Solano County:
• Hiddenbrooke Trail, Greater Vallejo Recreation Area
• San Pablo Bay Trail, Mare Island

Contra Costa County:
• Huckleberry Botanic Regional Preserve, EBRPD
• Mount Diablo State Park, CSP
• Los Vaqueros Watershed, CCWD
• Round Valley Regional Preserve, EBRPD
• Waterbird Regional Preserve, EBRPD

Alameda County
• Hayward Regional Shoreline, EBRPD. No dogs south of the West Winton Flood Control Channel.

San Mateo County:
• Año Nuevo State Reserve, CSP.
• Bair Island, Don Edwards San Francisco Bay Wildlife Refuge.
• Coal Mine Ridge, Portola Ranch Homeowner's Association.
• Cowell Ranch Beach, CSP.
• Edgewood Park and Preserve, SMCP.
• El Corte de Madera Creek Open Space Preserve, MROSD.
• El Corte de Madera Creek Open Space Preserve, MROSD.
• Fitzgerald Marine Reserve, SMCP.
• Huddart County Park, SMCP.
• Huddart County Park, SMCP.
• Sam McDonald County Park, SMCP.
• Memorial County Park, SMCP.
• Montara Mountain, SMCP.
• Pescadero Marsh, CSP.
• Phleger Estate, GGNRA.
• Portola Redwoods State Park, CSP (dogs are allowed in the park's campground, but not on the trails, except for Lower and Upper Escape Roads).
• Purisima Creek Redwoods Open Space Preserve, MROSD.
• Purisima Creek Redwoods Open Space Preserve, MROSD.
• Ravenswood Open Space Preserve, MROSD.
• Russian Ridge Open Space Preserve, MROSD.
• San Bruno Mountain State and County Park, SMCP.
• San Bruno Mountain State and County Park, SMCP.
• San Bruno Mountain State and County Park, SMCP.
• San Bruno Mountain State and County Park, SMCP.
• San Pedro Valley Park, SMCP.
• San Pedro Valley Park, SMCP.
• San Pedro Valley Park, SMCP.
• Sawyer Camp Trail, SMCP.
• Skyline Ridge Open Space Preserve, MROSD.
• Skyline Ridge Open Space Preserve, MROSD.
• Skyline Ridge Open Space Preserve, MROSD.
• Wilbur's Watch, Peninsula Open Space Trust.
• Wunderlich County Park, SMCP.

Santa Clara County:
• Henry W. Coe State Park, CSP (no dogs allowed at southern trailheads; dogs are permitted on one 1/2 mile trail only at the park's headquarters trailhead)
• El Sereno Open Space Preserve, MROSD
• Hidden Villa.
• Los Trancos Open Space Preserve, MROSD.
• Monte Bello Open Space Preserve, MROSD.
• Picchetti Ranch Open Space Preserve, MROSD.
• Rancho Canada del Oro Open Space Preserve, Santa Clara Open Space Authority.
• Rancho San Antonio Open Space Preserve, MROSD
. • Rancho San Antonio Open Space Preserve, MROSD
. • Rancho San Antonio Open Space Preserve, MROSD
. • Sanborn-Skyline County Park, SCCP, (dogs are allowed in the park's campground, but not on the trails)
• Shoreline at Mountain View, City of Mountain View.
• Sierra Vista Open Space Preserve, Open Space Authority.
• Stanford Dish, Stanford University.
• Upper Stevens Creek County Park, SCCP/MROSD.

Santa Cruz County:
• Big Basin Redwoods State Park, CSP (no dogs allowed on trails)
• Castle Rock State Park, CSP.
• Fall Creek Unit, Henry Cowell State Park, CSP.
• Wilder Ranch State Park, CSP.

San Francisco County:
• Batteries to Bluffs Trail, Presido San Francisco.

CCWD=Contra Costa Water District
CSP=California State Parks
EBRPD=East Bay Regional Park District
GGNRA=Golden Gate National Recreation Area
MCOSD=Marin County Open Space District
MROSD=Midpeninsula Regional Open Space District
MWNM=Muir Woods National Monument
PRNS=Point Reyes National Seashore
SCCP=Santa Clara County Parks
SCRP=Sonoma County Regional Parks
SMCP=County San Mateo Parks