There aren't any good just Indy online sources that I know of, but there are a few sites out there.
Indianapolis Railfan site
http://members.iquest.net/~tbonsett/rfipage.html
East Central Indiana
http://members.tripod.com/Caylorman/rail.htm
The biggest thing with Indy is the former Conrail/NYC now CSX Indianapolis Line from the east, then the St. Louis Line from the west. That is the biggest player. Avon yard is located as the name implies, west of Indy near Avon.
Conrail also had the Transfer and Hawthorn Yards, Transfer being on the west side of downtown, and Hawthorn being east of downtown on the old PRR mainline. Both were PRR yards, with Avon coming from the NYC, coming under full growth with the PC.
The Indiana Railroad runs the old IC from downtown to Illinois
The Indiana Southern operates the former PRR out of the southwest side of Indy.
The Lousville and Indiana operates the former PRR from downtown to Lousiville.
I never worked out of Indy, so I can't tell you much about operations.
CSX had the former B&O in from Cincy/Hamilton, this is used by Amtrak too.
The other is the former I&F leaving the old PRR at Davis and heading north, flying over top the NYC mainline, with full connector tracks, then the line splits just north of that at Clearmont, the Amtrak uses the line that heads to Crawfordsville, and CSX still uses the other line to Frankfort.
The old Monon is gone, and the former NKP IMC line is used by the Fair train and museum located north of Noblesville.
So basically the run down of abandon lines
PRR from Hawthorn yards east is gone, both freight and passenger mainlines.
The belt track the runs from the northeast side to the north west side around the south side of town.
The old NYC Springfield line is gone just outside of town, currently used as an industrial lead.
The former NYC mainline to Cincinnati is still in use, CSX has it and RA has rights over it. Amtrak uses what is left of the Beech Grove facility on the southeast side of town.
The L&I comes up the former PRR line from Louisville and connects in to the NYC Indianapolis line at IU, which is at the union station.
There are more, hopefully someone else can fill it in, gotta run.