This is a potentially neverending list.

In no order:

• Interactive map that shows origins of SF place names.
• The Anti-Eviction Mapping Project.
• Awesome geographer Eric Fischer has created lots of amazing maps of SF (and other places).
• Creek and watershed maps of SF from the Oakland Museum of California.
• SF bike map (PDF)
• 20 neat maps here.
• Freeways: the Freeway Revolt and freeways never built and freeways unbuilt after the Loma Prieta earthquake.
• This Quora highlights some really cool maps:
  • Stamen Design makes a lot of neat maps. Here's a cool one from Shawn Allen, a partner at Stamen.
  • The islands of San Francisco by Burrito Justice.
  • 3D topography of crime visualizations in SF.
  • maps created by uber of where people take trips.
  • SF surface rail map in 1934 (primarily electric streetcars). Here's the related article.
  • Inequality and mass transit (what transit stops are the most and least unequal?)
  • 2010 atlas of HIV/AIDS in SF created by the San Francisco Department of Health
  • Psychogeography of SF neighborhoods (created by 7x7 Magazine)
  • Visualizing Mental Maps of SF by Yo-Shang Cheng and Rachelle Annechino at the UC Berkeley School of Information
  • Mission Possible - 20 maps of the Mission created by undergrad students in the Cartography and GIS Education Lab in UC Berkeley's Geography Department
  • SF trees heat map - based on the location of over 100k trees!
• Map showing SF's oldest buildings

Historic maps

• Old SF - 16,000 historic photos (from 1850-2000) of SF put on a map.
• 1905 Sanborn maps of SF - awesome interactive
• 1938 aerial photo map
• "Old Maps of San Francisco Guaranteed to Blow Your Mind"
• Also, the David Rumsey Map Collection has all kinds of historic maps, not just about SF.

Literary maps

• Really neat interactive map of literary places, booksellers, places in books, author homes, etc. including pictures of what some of these places are like now.
• Literary City: a neat poster that shows passages from books on different SF neighborhoods.

Art maps

This is a list of maps found in a post in Reddit's San Francisco subreddit). The original post was made by oxidiz (a very interesting-sounding San Franciscan...who may be a nice person to contact regarding this here LocalWiki site?). The original post is found here. The following text is quoted from the original post. Would you be so kind as to start reformatting this page so that it is no longer mostly copypasta?

Ork Posters The first map that started the collection, mine is in green. No longer a favorite per se, but part of the series

Jennifer Maravillas by Jennifer Maravillas. I love the color palette. I think they once sold this printed on a silk scarf as well

Burrito Justice Burrito Justice’s indispensable ‘Islands of San Francisco’ neighborhood map. Love the infographic style. It’s printed by Zazzle, pay the extra for the Archival Heavyweight matte paper, it’s worth it.

Blue is the Land Stunningly simple deconstruction of the city, neighborhoods by size

Axis Maps Typographic map, the letterpress editions are beautiful and sadly sold out, mine is blue, but the color print is available and multicolor adds another dimension to the piece Axis Maps - letterpress sold out

I Lost My Dog A groovy lettering scheme for this poster. Check the green or blue palettes, rainbow may be a bit too…much

Archie Press Another simple neighborhood map, imagined with circles. i like the red ink on brown paper

JazzBerryblue Another great artistic map poster of the block grid

SF Electric Works The Literary City, for poets, dreamers and scribblers

Urbane Maps Neighborhoods described in words

Abe Bingham My most recent addition. This is a highly detailed topographic map of the city, just released for general sales after a successful kickstarter campaign

[Updated 1/30] to include suggestions from the comments below

Doug McCune If San Francisco Crime were Elevation. Great visualization of the city's own crime statistics, circa 2009. Not available as a poster, but a terrific example of scraping datasets and visualizing it with maps.

Stamen Design Studio makes this watercolor overlay for Google Maps. They also do lots of other cool things with maps and data visualization. Check em out! Also not available for printing.

Sarah Schulz Ghostly interpretation of the city, only the buildings are represented, parks and roads disappear from view.

Dry Well A porcine view of a city. The tagline is 'San Francisco is for Carnivores'. Pair it with a membership to the Boccalone Salumi Society for the 'Tasty Salted Pig Parts'

These Are Things neighborhood map. Informative and quality production. Not among my very favorite designs, but it's in the collection. I really dig their modern world map in the black and grey color scheme.

Line Posters Not a San Francisco specific map, but this graphic design of the Bart/Muni/CalTrain commuter rail lines is pretty great and comes in a nice selection of colors.

Jennifer Maravillas Silk scarf map art of San Francisco. This one is sold through The Bold Italic store and is the same design as the poster listed above. A lavish gift for your lover in your lovely city. Currently out of stock, they expect deliveries in a couple weeks.

Bloom Screen Printing Beer Map of San Francisco. Where to buy it, where to drink it, where it's made. Sadly they excluded the legendary SF Brew Craft but it's still a great and inexpensive piece of art.

Rebecca Solnit Infinite City: A San Francisco Atlas, recommended by /u/westcoastwomann . I look forward to reading it!

[Updated 1/31]

Wood Cut Maps It's not a poster, but hey, it's a representative map of San Francisco you can slap on your wall. This seller has a 'Design Your Own' feature that allows you to pick the area of the map. Or you could even make one of just your neighborhood.

Dave Marcoullier Another map made of wood. Very attractive layout, nice bevel. Reasonably priced too.