I'll add a few.
In 1850s, the U.S. Government conducted a series of land surveys in order to find the best route for a Trans-Continental railway to the Pacific, and ultimately found the southern most proposed line was the best. The Gadsden Purchase was done in order to secure the territory needed to build it, but then the increasing sectional disputes between the North and the South killed it the project until the 1870s.
Even then, the Central Pacific monopoly managed to screw it over. Had it been built, as was originally intended, it would've roughly followed the route of what IOTL became the Butterfield Overland Trail:
The main difference would be, instead of connecting up towards San Francisco, it would've directly terminated in San Diego (Another spur would, most likely, later connect it to San Francisco). Such an advantageous position, in terms of being an excellent port and a terminus for the first Trans-Continental Railroad would've turned San Diego into the premier city and port on the West Coast. As was noted IOTL by the opponents of the 1870s effort:
It was at this moment that Stanford, in an interview published in the San Francisco Chronicle, first set forth publicly the plan to push the Southern Pacific from Yuma across into Texas. In concluding his interview he said: "The people of San Francisco will never appreciate how great a danger menaced them . . . Had Tom Scott built his road to the Pacific he would have taken from us our best prospective traffic and carried it East . . . He would have given San Francisco a blow from which she would never have recovered."
So basically San Diego ends up as
the city in California, with Los Angeles never coming into being as a major city and San Francisco slowly dying off in the 19th Century before the earthquake in 1906 finishes it off.
Shifting back east with this, the most likely Eastern origin point for the railroad is Memphis, due to the shorter route it offers and
the fact there was already some existing track in the region to build from. Such would, between the rail traffic and Mississippi River trade, make Memphis the main city along the river and definitely so in Tennessee. Depending on when the Civil War gets fought if it's not prevented, such might make Tennessee Unionist enough to prevent its secession, although I personally doubt such given how West Tennessee was politically at the time.
Some more, either in this proposed ATL or on their own:
Richmond, Virginia - In the event of no Civil War, or at least Virginia not getting as smashed by it, Richmond would definitely be a greater city without having to be rebuilt and the continued status of West Virginia in the Commonwealth would likely prove a boon to industrialization, as the resources of the aforementioned state would be flowing to Richmond.
Big Stone Gap, Virginia - Change the Civil War (Averted or quicker ending) or remove Alexander Arthur, and such would've made available the capital needed to carry out the industrialization plans for the town. Such would've nerfed Middlesboro in Kentucky and perhaps Kingsport, Tennessee later on as Eastman Kodak might be more interested in developing its plant in the growing BSG. I personally don't think it could've become a Pittsburgh as was extolled, but a city of 50-80,000 with a strong industrial basis certainly seems possible. Such would've also kept the nearby coal towns relevant and large, first as sources of coal for iron/steel production, and then as suburbs as the town became a city. Add in UVA deciding to locate their affiliate campus here instead of Wise, and you'd definitely have the Virginian version of Johnson City, but with the industry of Kingsport thrown in.
Middlesboro, Kentucky - As kind of a reverse of the above, avert the 1890 Fire and have Barings not make such bad investments in Argentina, and Middlesboro could end up bigger than it did. If capital keeps flowing in, the railroad tunnel can be built and thus the city could become an important hub between Knoxville and Lexington, but the plans to turn it into a major industrial site were always going to fall short due to the poor quality of materials in the area. Overall, it could probably reach a size of 20-30,000.
Fort Blackmore, Virginia - I've never been able to confirm such, but a High School history teacher of mine stated that Eastman Kodak nearly built what became their Kingsport Plant in or near this tiny hamlet, but were stopped by some of the local tobacco growers. Had they failed, Fort Blackmore probably could've grown into a city of 30,000-40,000.
Johnson City, Tennessee - If you can somehow avert the Panic of 1893, Johnson City would continue to grow in size, and
might be able to turn itself into a second Knoxville.
Muscle Shoals, Alabama -
I'll let the town itself explain what nearly happened:
In 1921, automotive tycoon Henry Ford, accompanied by Thomas Edison, came to Muscle Shoals with a vision of transforming this area into a metropolis. “I will employ one million workers at Muscle Shoals and I will build a city 75 miles long at Muscle Shoals,” stated Mr. Ford. The instant rumors of Ford’s plan hit the streets, real estate speculators began buying up land and parceling it out in 25 foot lots and putting in sidewalks and street lights. People from all over the United States bought lots, sight unseen, during this time. Mr. Ford’s offer to buy Wilson Dam for $5 million was turned down by Congress. (The initial cost of the construction of the dam was $46.5 million.) Instead, Congress, under the influence of Senator George Norris of Nebraska, later formed the Tennessee Valley Authority to develop the dam as well as the entire river valley. Senator Norris felt strongly that the public, rather than private companies, should receive the benefits from the government’s investments in Muscle Shoals. Although Ford’s plans did not turn Muscle Shoals into a huge city, it did lay the foundation for the city of Muscle Shoals.
So kill off Norris, and you might be able to get a second Birmingham.
Mobile, Alabama - After the Civil War, trade began to shift away from the Mississippi and New Orleans lost some of its prominence in this regard. Had it got hit by a sufficiently strong Hurricane sometime in the 1870s-1890s, it's possible Mobile could've replaced it as the premier port on the Gulf, given its central location and proximity to the iron production sites at Birmingham.
Birmingham, Alabama - Avert the Civil War or have it won by the South, and Birmingham would've turned into every bit the rival of Pittsburgh that it was intended to be. Due to unfair Pro-Pittsburgh pricing rates forced into usage, Birmingham's ability sell was deeply undermined, and this was further compounded by the lack of sufficient regional capital to draw on due to the effects of the Civil War.
The Iron and Steel Industry of the Birmingham, Alabama, District by Langdon White (Economic Geography, Vol. 4, No. 4 (Oct., 1928), pp. 349-365) outlines the areas Birmingham would've easily been able to out-compete Pittsburgh in
at the minimum:
Chicago, Illinois - Yes, I know it was already great, but it certainly could've been greater,
had it successfully managed to become the center of American automobile production.
Duluth, Minnesota - U.S. Steel apparently narrowly chose expanding production in Pittsburgh over Duluth in 1911, a move which, if reversed, certainly would've brought more development.
Topeka, Kansas - Had it got the international airport over Kansas City, it could've went the Atlanta route of development.
Portland, Oregon - In the 1960s they tried to build a stadium to attract the Raiders and made a bid for the 1968 Olympics, but both ended up failing. Had they not, it would've obviously been a boon for the city.