It might surprise you to know that a city with a population density of 17,383 people per square mile has an abundance of hiking trails. As a matter of fact, a significant amount of San Francisco's city space is set out as park land. In fact, the National Park Service operates "Golden Gate National Recreation Area" which encompasses beaches, trails, and historic sites. I was pleasantly surprised to find myself going on a legitimate trail run within the city limits and pretty much having it all to myself. Here are some sights I recommend

Trails run through the west side of the city and through WWII era installments
The Presidio of San Francisco

Most people believe California somehow came into existence during the 1950's and hippies later colonized the new land; this is false. The Presidio of San Francisco was a Spanish military base established in 1776 the same year the United States was founded. Three different countries have claimed it since then, Spain, Mexico, and the United States and at one point it was an active military base. Far too much has already been written about the history of the Presidio to be contained here, but it should be noted that it is well worth the visit. The buildings within the park are the antithesis of San Francisco architecture; the houses are large and colonial with an austere feeling to their design. There are expansive yards and many buildings that are hundreds of years old. The trail system is mostly towards the beaches but a walk through the Presidio will not feel like traditional San Francisco.
The Presidio is a much older part of San Francisco
 Alcatraz Island

Alcatraz Island is the most famous prison in the United States. The short story is that pretty much every single 1930's who's who in the criminal world was a prisoner at one point in Alcatraz. The most interesting part about visiting the island is learning about all the true escape stories from Alcatraz. While no one has ever been found to have escaped, the stories of how they tried it are fantastic. The island has been featured in many films such as "Escape from Alcatraz", "The Birdman of Alcatraz" (great Burt Lancaster film) and "The Rock" (ehh... maybe not so great). But in reality, there is a rich amount of history around Alcatraz Island making it well worth the visit. It is also nice to hike around the island away from the city although I doubt the past prisoners enjoyed the same freedom.
A very strategic location for a prison
"Hiking" the Golden Gate

Its sounds like somewhat of a joke, but hiking the Golden Gate Bridge can be a difficult affair. Its about a 3.5 mile hike round trip across the bridge but it has wild weather. Seafarers know that it is a very difficult task to cross into the bay from the ocean due to the fog, wind and wild currents. While you don't have to worry about the ocean on the bridge, be prepared for cold weather and very strong winds. However, this is a classic San Francisco adventure and its something every visitor must do before leaving this beautiful city! Pack some warm clothes!

Angel Island: I'm almost embarrassed to say this, but I've never been to Angel Island, another hiking destination within the San Francisco Bay. If you have been, I would love to hear about your experience!

No shortage of hills!
So get out there and enjoy a city that has some real "urban" hiking!

Read. Plan. Get Out There!