Savona. The Delaware, Lackawanna and Western Railroad (DL&W) was completed through Savona in 1882, providing direct competition with the Erie Railroad, which opened in Savona in 1852. The opening of a second major railroad convinced a majority of the residents that the town would continue to grow and need its own government. May of 1883 Savona became a village corporation.

Atlanta, A hamlet in the northeast part of Cohocton formerly known as "Bloods." It was founded around 1840. The Cohocton River changes from east-flowing to south-flowing at Atlanta.

The settlement of the township was slow at first. There were many dangers and hardships: bears, bobcats, panthers, lynxes, wolves and rattlesnakes.

Avoca, The first settler arrived around 1794. At that time, the area was home to the Seneca Indians. The town was formed from parts of four other towns in 1843: Bath, Cohocton, Howard, and Wheeler.

Monroe was once the site of the Great Northern Railway's botanical gardens where fresh flowers for their passenger trains were once grown. Each day these flowers would be loaded aboard the Western Star for distribution throughout the system so that each dining car passenger might have fresh flowers with their meal.
http://nwownrailfan.com/archives/features/0202camp.html

The Little Traverse Bay area was long inhabited by indigenous peoples, including the Odawa people. The name "Petoskey" is said to mean "where the light shines through the clouds" in the language of the Odawa. After the 1836 Treaty of Washington, Odawa Chief Ignatius Petosega (1787–1885) took the opportunity to purchase lands near the Bear River. Petosega's father was Antoine Carre, a French Canadian fur trader and his mother was Odawa. By the 1850s, several religious groups had established missions near the Little Traverse Bay.

January 5 & 6, 1885 Leiderkranz Hall 

Interviewed 5 January 1885 "A Great Humorist," Louisville Post 5 January 1885, p1  

Included in "Mark Twain: The Complete Interviews" (#31) The Galt House: Built in 1835 at the corner of Second and Main on the Louisville waterfront. 

Cumae (Ancient Greek: Κύμη (Kumē) or Κύμαι (Kumai) or Κύμα (Kuma); Italian: Cuma) was an ancient Greek city on the coast of the Tyrrhenian Sea in Campania, Italy. Cumae was the first Greek colony on the mainland of Italy and the seat of the Cumaean Sibyl. It was the Cumaean alphabet that was adopted in Italy, first adopted and modified by the Etruscans (800–100 BC) and then by the Romans (300–100 BC), thus becoming the Latin alphabet, the world's most widely used phonemic script. The Cumaean alphabet was also used throughout the Greek island of Euboea.

Asnières-sur-Seine was originally known simply as Asnières. The name was recorded for the first time in a papal bull of 1158 – as Asnerias, from Medieval Latin asinaria, meaning "donkey farm". The poor soil of Asnières, where heather grew in medieval times, was probably deemed suitable only for the breeding of donkeys.

Twain made a day-trip from Como to Chiasso in nearby Switzerland, not mentioned in Innocents Abroad (Mark Twain A to Z)

Sam and companions merely passed through by train on their way to Venice, July 20, 1867.
Mark Twain Project: Quaker City Itinerary

The first records of the area date back to the IX century in the Lombard period. The position of the town was strategic for enemies attacks during the Middle Age. Lately, the town became an important cultural and religious center. It was home for many Bishops until the 1973 when the Diocese of Campagna merged with the Archdiocese of Salerno.

Twain writes of Going to a town called Annunciation prior to his climbing Mt. Vesuvius. Torre Annunziata is the only locale I can find nearby Naples that fit his description.

Torre Annunziata is a city and comune in the province of Naples, region of Campania in Italy. It is located on the Gulf of Naples at the foot of Mt. Vesuvius.
https://en.wikipedia.org/wiki/Torre_Annunziata

Beyoğlu (Turkish pronunciation: [ˈbejoːɫu]) is a district located on the European side of İstanbul, Turkey, separated from the old city (historic peninsula of Constantinople) by the Golden Horn. It was known as Pera (Πέρα, meaning "Across" in Greek) during the Middle Ages, and this name remained in common use until the early 20th century and the establishment of the Turkish Republic.
https://en.wikipedia.org/wiki/Beyo%C4%9Flu

On September 3, 1867, a party from the Quaker City, likely including Sam, visited Scutari during the day. Mark Twain Project: Quaker City Itinerary

Galata was a neighbourhood in Constantinople (today's Istanbul), located at the northern shore of the Golden Horn, the inlet which separates it from the historic peninsula of old Constantinople. The Golden Horn is crossed by several bridges, most notably the Galata Bridge. The medieval citadel of Galata was a colony of the Republic of Genoa between 1273 and 1453. The famous Galata Tower was built by the Genoese in 1348 at the northernmost and highest point of the citadel.
https://en.wikipedia.org/wiki/Galata

Balaklava (Ukrainian: Балаклава, Russian: Балаклава, Crimean Tatar: Balıqlava) is a former city on the Crimean Peninsula and part of the city of Sevastopol which carries a special administrative status in Ukraine. It was a city in its own right until 1957 when it was formally incorporated into the municipal borders of Sevastopol by the Soviet government. It also is an administrative center of Bakalava Raion that used be part of the Crimean Oblast before it was transferred under the Sevastopol Municipality.

Beer-Sheva (/bɪərˈʃiːbə/; Hebrew: בְּאֵר שֶׁבַע‎ About this sound Be'er Sheva [beʔeʁˈʃeva]; Arabic: بئر السبع‎‎ About this sound Bi'ir as-Sab [biːr esˈsabeʕ]) is the largest city in the Negev desert of southern Israel. Often referred to as the "Capital of the Negev", it is the center of the fourth most populous metropolitan area in Israel, the eighth most populous city in Israel with a population of 203,604, and the second largest city with a total of 117,500 dunams (after Jerusalem).