I would say any city with connecting rail service to Amtrak should count. My top choice college, Northwestern, is in Evanston, Illinois, a town without Amtrak service. However, there is frequent Metra and CTA rail service to downtown Chicago where they connect with a short walk to Amtrak. Glenview station is even closer, although there is no direct rail service between Evanston and Glenview, in addition to the fact that Glenview is a stop on only the Empire Builder and Hiawatha Service. Contrast this to other towns, where Amtrak may stop in the same city as the college but is not within walking distance and lacks effectiveness public transit if any exists whatsoever. One example of this is the University of Central Florida. Although it is in Orlando and relatively close to both the Orlando and Winter Park stations, there is not convenient public transit to either.
I have actually done this exact connection with Metra on the UP North Line from Evanston, IL to catch LSL 49 to Springfield, MA in June 2016. It was a pretty easy connection, though the walk from the Metra stop at Olgivie Transportation Center to Chicago Union Station is not very well marked.
One could always take the #208 Pace bus west to Golf/Waukegan to get off, then transfer to the next northbound #210 bus to get up to downtown Glenview. Or another idea is to take the #208 bus to Golf/Harlem, and then the #423 bus northbound till you got to Glenview. You could do vice versa to get back, though I'll note the #210 and #423 buses end early in the evening on weekdays, and that it has NO weekend service. I sometimes have on weekends(when desperate) taken the #208 Pace bus along Golf Road to Harlem, then walked the 25-30 minutes north into Glenview! Or vice versa back after getting off at Glenview, providing I walked to Golf/Harlem in time before the last eastbound #208 bus.
Since I know that strategy isn't for everyone, you might just be best(if it's a weekend/holiday, or if it's too late in the evening on a weekday) to request an Uber/Lyft car from Glenview, to get back to Evanston. Or vice versa, to get from Evanston up to Glenview.
Isn't South Bend college town?
Notre Dame is in the town of Notre Dame, but it borders South Bend; I think it is close enough.
University of Notre Dame is definitely within South Bend, IN. It is NOT it's own separate town from South Bend, not sure why you thought that. There are a few nearby municipalities outside of South Bend though, such as Roseland(this is a very tiny one most people forget about), Mishawaka, and Granger to name examples. And yes a lot of people do take the South Shore Line besides Amtrak to get to South Bend, since the fare is cheaper(vs. Amtrak) from Chicago.
Moving on, I'm surprised noone has mentioned all the Illinois colleges(public and private) that are served by Amtrak. Which include Knox College in Galesburg, Western Illinois University in Macomb, Illinois State University in Normal(not to forget Illinois Wesleyan in Bloomington), University of Illinois at Springfield(UIS) in Springfield, Olivet Nazarene University in Kankakee, University of Illinois(UIUC) in both Champaign and Urbana(IIRC, the college has buildings in both communities), Eastern Illinois University in Charleston(NOT technically right on Amtrak, but I've heard of students who get rides or bike between Charleston and Mattoon on a bike path between those communities to board the train there), and Southern Illinois University in Carbondale. Don't forget the Champaign-Urbana/Carbondale, and also the Galesburg/Quincy line have 2 trains in each direction a day, and 4 trains a day overall(not counting the long distance Southwest Chief and California Zephyr). For the Chicago-Saint Louis line(serving Bloomington-Normal and Springfield), there are 4 trains a day in each direction, and 8 overall(excluding the Texas Eagle, and from my personal experiences I'd be careful about riding that train since it often runs late).
The other colleges that jump to my mind in the Midwest served by Amtrak include Western Michigan University in Kalamazoo, Michigan State in East Lansing, University of Michigan in Ann Arbor, Marquette and University of Wisconsin-Milwaukee in Milwaukee, Viterbo University and University of Wisconsin-La Crosse in La Crosse, WI, Winona State University in Winona, MN, University of Minnesota and Macalester College not far from the St. Paul stop(plus I suspect more I'm forgetting), Purdue University in West Lafayette(you'd get off at Lafayette, and it's across the river), and IUPUI and Butler University in Indianapolis. Wouldn't be surprised if I'm forgetting some other Midwest colleges, but unfortunately some places have graveyard train arrival times(i.e. Cincinnati having both only a late at night Cardinal train and only 3 times a week, Fargo, ND having the daily Empire Builder come in both directions late at night, etc). I think Saint Cloud, MN has a Minnesota public college too(a la Winona), but the train times are early in the morning and late in the evening. Not as bad as Fargo's train times for the EB, but keep that in mind.