I grew up there, but haven't been in a long time so I can't speak for dining and such. Other than the train rides, here's some stuff to see:

• Jim Thorpe's monument on the east side. It's on 903 past the main part of town on your left. Olympic gold medalist in the pentathlon and decathlon, NFL hall-of-famer (so much that it's his statue at the front doors to the Hall of Fame), Major League Baseball player, pro basketball player, it's hard to argue that he wouldn't be the greatest athlete of all time. Nothing to do with the town except that here's buried there, though.
• Downtown, go down Broadway and on the right is the old County Jail. It's cool for the tours and ghost stories. Charles Neast, the old Sheriff, went to my church when I was a kid (probably died around 1990) and he swore the phantom handprint was legit.
• Also downtown, Race St has a quaint European vibe and is filled with little shops.
• The Asa Packer and Harry Packer mansions on Packer Hill at the bottom of Center Ave have tours and are pretty cool. In winter the street might be one-way for safety reasons (it's a pretty steep hill) so watch out.
• Outside of downtown 209, Flagstaff has a scenic overlook of the town. Was a night club and restaurant at various times. I have no idea what's up there nowadays.
• If you're into creepy, there's an awesome cemetery in the heights on South Ave next to the Lutheran church that you can walk through and see the monuments.
• If you're into hiking and risk-taking, you're definitely not allowed in Glen Onoko Falls. It's closed off and too dangerous. Do not cross the river and take a left off 903 to Lehigh Gorge State Park at the bottom of the trail.
• For less risky, but a bit more boring and less scenic hiking, the historic Switchback Trail is in the heights, and can be accessed off Center Ave, IIRC.