San Luis by Gregory Alan Isakov who I saw live only a few days ago. Maybe I didn’t think of it because he didn’t perform it. He did however do Amsterdam.
Olympia by Hole
Which is actually not a city, so I guess doesn’t count?
Calcutta, a German pop song that was a hit for Lawrence Welk in 1961.
Abilene, a hit for George Hamilton IV in 1963.
Riverside – Beat Farmers
Bowling Green by The Everly Brothers
Houston by Dean Martin
San Diego by Blink-182
Cleveland by Jewel
Gainesville by Tom Petty
“Houston” by R.E.M. or Soul Coughing
“Compton” by Kendrick Lamar (feat. Dr. Dre)
“Pompeii” by Bastille or Sleater-Kinney
“Rome” by Phoenix
“Budapest” by George Ezra
Since dropping subtitles seems okay:
“Yorktown (The World Turned Upside Down)” from Hamilton
You mean “Woman from To-Kay-Yo”? 
La Grange, ZZ Top
Houston, The Gatlin Brothers
Dallas, Alan Jackson
Salt Pork, West Virginia–Louis Jordan
“Mill Valley” by Miss Abrams and the Strawberry Point Third Grade Class (one of the cheesiest songs to ever make the Billboard Top 100)
“Baltimore,” written in 1927 by Jimmy McHugh, Irving Kahal and Dan Healy, and recorded by Clarence Williams, Fletcher Henderson, and several others. This song is actually about a dance called the Baltimore. Are there any more Baltimore songs?
Gus Kahn and Tolchard Evans wrote a song called “Barcelona” in 1926, but I don’t know of any famous recordings of it.
Luchenbach, Texas by Waylon, Jennings
That was what I was going to say. It makes the city in Indiana sound way more of a tropical paradise than it actually is.
Yeah! And why can’t we post our favorite types of onion? What’s up with that?
Dublin, by Thin Lizzy
Vidalia
mmm
If that’s OK, then Odessa (City on the Black Sea) by the Bee Gees could be included. But there is also a song titled simply Odessa by Caribou.
That’s interesting, because the Champaign Illinois by the Old 97s that I listed in the OP is basically a reworking of Dylan’s “Desolation Row” with new lyrics. So Dylan is connected to two completely different songs named Champaign Illinois!
“Gary Indiana” from The Music Man
“Syracuse”–Pink Martini
Philadelphia by Springsteen
Oops, it is actually “Streets of Philadelphia”.