Best I've played by far is Pacific Grove Golf Links near Monterey
I've played River Cut and will agree that it's one of the best Munis I've played (at least among the ones that don't host Majors). Chambers Bay is a little bit of a stretch as a Muni--it's basically a marketing campaign, as they built a "city" course specifically to host USGA Championships, and it has caddies.
No one has mentioned Memorial Park in Houston. Great course, and truly a "city" course. It's in the middle of a very large city park, has hosted numerous pro events (and still hosts big amateur tournaments). The tennis complex in the park also hosts a pro tournament.
Have played two of those in the last year.
Hulman Links in Indiana was in terrible shape. I think the combination of two hot, dry summers and an under funded small-town maintenance budget took a big toll. I'd definately play it again for the $20ish they charge but would be a stretch for it to make any best in state lists in its current condition.
Played Superior National in Minnesota last fall. The views of the fall colors in the national forest and the views of Lake Superior were awesome. Course was also in great shape. Won't say it is a great design but it was an absolute pleasure to play. Only real complaint is that the lay out is almost impossible to walk and the cart does take away from the northwoods experience.
If my work travels will allow hope to play either Landsmeer in Iowa or Glacier Wood in WI this summer. Good muni golf in small communities is something I seek out every chance I get. The atmosphere just suits me.
San Antonio has some great muni courses. Brackenridge is where Souchak broke the scoring record - and site of the Texas Open for many years. Cedar Creek, another very good course. There are so many to list, but SA was one of my favorite places to live not only because of the culture, pretty women, Spurs, but because of the great golf there.
Sorry, but that list is completely wrong. Denver's city park is flat boring course. If you really want a good muni course in Colorado, there are tons of courses owned and operated by city of Aurora (Saddleback, Murphy Creek), city of Golden (Fossil Trace) and Lakewood (Fox Hollow) that have fantastic views and layouts.