The highest point in Marion county (Indianapolis) is in Crown Hill Cemetery. Enter at 34th and Boulevard Place. The hill isn't long, but it's steep. It might be useful when worked into some sort of hill workout. I run there at times. Kind of an interesting place. Lots of famous people buried there (John Dillinger, President Harrison, etc).
There's some nice rolling hills in Cool Creek park, located at 146th street kind of near the Wal-Mart where Carmel/Westfield come together. Fair warning, this park seems to be a homosexual hangout, so if it bothers you to see cars backed into spaces, and strange men ogling you, stay away.
For flat trails, the canal path can't be beat. Catch it on the north end in Broad Ripple (62nd/Broad Ripple Ave) and College. The south end terminates somewhere around 30th street, near the old Naval armory.
There's always the Monon for flat and good scenery. You can run this from downtownish all the way up to 146th street. Paved, but I usually run in the dirt/gravel alongside the path to save on leg wear and tear.
Eagle Creek is wonderful, if you're out that way (I'm usually not).
The canals downtown are kind of interesting, but you'd be pouding out on concrete and it's not terribly long.
Ask more questions if you have them...I've lived here 10 years and know the area pretty well.