My daughter (6 years old) absolutely loves the park trains at Bowcraft and Jenkinson's. I have not yet taken her to Turtle Back Zoo, but now have an extra reason to try.
When I was a kid, my dad used to take my brother and I to Becker's Farm. Damn, I miss those trains. I've gotta use the "daughter excuse" to head up to P-Burg.
One "park train" I haven't seen mentioned here is at Northlandz in Flemington
http://www.northlandz.com. Their Web site says: "The Raritan River Railway: This 2/3 scale steam replica travels through tunnels and over bridges to give you a relaxing ride through our nature rich woodlands. (completion fall 1998)." I have seen this train from Rt. 22 while passing by, but I have not yet been in the area when I had time to stop. The Web site also mentions a 1-mile model train layout.
More on park trains:
http://www.trainweb.org/parktrains/index.html
http://www.nnerailsystems.com/parktrain ... ast_1.html