There are seemingly endless opportunities in the bay area when it comes to outdoor recreation, and whatever you're looking for, it's most likely within an hour drive or less. I've begun to seek out the local parks on the Peninsula and found a few I really like for running. Crystal Springs has to be my favorite so far for a couple reasons, it's flat with paved and unpaved trails, the views of the lake and mountains are fantastic, and you'll feel distant from the city even though an interstate is just minutes away (Pictured right - San Mateo Parks Website).
Other places I've been are Edgewood Park, Coyote Point, Mirada Surf and Pillar Point. By the end of the year, I intend to see all of the San Mateo County Parks. Check out their website, they've really done a nice job putting together detailed information, pictures and trail maps!