According to "rental marketplace" Lovely, though we here in San Francisco feel that we have dreadfully high rents, it could be worse: we could live in Palo Alto.
The company's Q3 Rental Market Report, which is based on "aggregated rental inventory posted on Lovely between January 2012 and September 2014, and is no longer active," (keep that in mind — it's not a completely comprehensive report based on all rental listings in any area, just the ones that appear on their site) says that Palo Alto tops the nation, with a median rent of $3,645. SF is second on the list, with a median of $3,488, a 3.3% increase from last year.
But just because Palo Alto beat us on the median doesn't mean that we still don't have some standouts: according to their report, the priciest nabe in which to rent in SF is Presidio Heights at a median of $5,100. #2 is Dogpatch ($4,300). Cow Hollow and Russian Hill are tied for #3 at $4,200. If you're feeling cheap, then head to Mission Terrace, where the median rent is "only" $2K, the lowest in the city.
You can read their full report, which is chock full of graphs that basically say "everything is very expensive" here. Chart of SF median rents by neighborhood: Lovely