Proctor Springs--This part of Cameron Park is immediately adjacent to Lindsey Hollow Road. When you're going down the road from Herring Avenue, the entrance will be on your right. There are lots of stories of that place being haunted, maybe because of its proximity to Lindsey Hollow Road.
A friend of mine who grew up here and is a paranormal enthusiast one of the creepiest parts of town is what she calls "the cul-de-sacs." It's three streets--Algonquin, Seneca, and Avondale Avenues--off of 18th Street that end in, well, cul-de-sacs, which is strange for a neighborhood of its age. It's definitely freaky down there at the ends of the streets at night, but I couldn't give you any specific house to look for.
City Hall--3rd & Austin. Look up the Waco Horror online; it's everywhere. A young black man named Jesse Washington was lynched and burned by a violent mob there in 1916 after he was accused (falsely) of murdering a farmer's wife in Robinson and drug out of the courthouse where he was on trial. The current city hall is not the one that was there at the time, but it's on the site of the old one.
Old Waco High School--8th & Columbus. My local enthusiast friend knows of spirits here, too, in the city's abandoned former high school.
Texas Ranger Museum and Hall of Fame--In Fort Fisher Park, University Parks Drive & I-35. When the city started adding onto the museum, which was built in the 1960s, workers uncovered human remains. Turns out, the complex sits on top of the old 1st Street Cemetery and quite a few graves weren't moved, as people have always assumed they were 40 years ago. There are also lots of marked graves more towards University Parks Drive that are part of First Street Cemetery, plus there's a Jewish cemetery right next door.
You might also check with the Historic Waco Foundation. It owns and maintains several historic old homes around town. I'm sure some of the staff have stories.
Around the turn of the 20th Century there was a licensed Red Light District in Waco called "The Reservation." It was between Washington and Jefferson Avenues and 3rd Street and the Brazos River. It's mostly an empty field now. At 3rd & Jefferson is a mission-style Catholic church (not as old as it looks) and behind it, on Barron between 3rd and 4th is what used to be a convent. It's now apartments.
Just a few suggestions for interesting locales. Happy hunting! There's bound to be something just about anywhere you turn here.