Near Louisville KY overnight out and back.

In Indiana, the German Ridge Trail (Hoosier NF) is about a 20 mile loop, with multiple cutoffs if you decide to cut it short. Some of it has been recently logged but most is in pretty good shape.

Adventure Hiking Trail is about a 24 mile loop, more strenuous, water is usually in short supply. A bit closer to Louisville.

Deam Wilderness, also in the Hoosier, is our only Wilderness Area in Indiana – though it's a lot less wild then you'll find out west. Plenty of trails including some that aren't on the official maps. Some nice camping spots on the shores of Lake Monroe.

Knobstone Trail, also close to Louisville, is 48 miles with plenty of spots you could do an out-and-back. Has a reputation of being tough, I haven't been on it yet.

I haven't had a chance to hike the Daniel Boone yet so no opinion there.

The Red River Gorge is in the Daniel Boone National Forest and has some great possibilities for an overnight. But it's a 2.5 to 3 hour drive from Louisville. Also, the gorge can get a little crowded in late September. There are other possibilities in Daniel Boone National Forest, too. It's been a long time since I have been up there, but you can find some recommendations on routes on the internet. Backpacker.com has published several articles on routes through the gorge, so you may find some good suggestions there.
Here's a link to a trip report on backpackinglight: http://www.backpackinglight.com/cgi bin/backpackinglight/forums/thread_display.html?forum_thread_id=32225

And here's another with some trail ideas: http://www.backpackinglight.com/cgi-bin/backpackinglight/forums/thread_display.html?forum_thread_id=32881

There are black bears in DBNF, and the forestry service has issued a food service restriction.

I have hiked most of the longer trails in the portion of Hoosier National Forest that lies south of Interstate 64), and, although I have enjoyed day hiking there, I have not felt particularly inspired to do an overnight, at least in that part of HNF. Ticks are bad there, too, that time of year. The Deem, which is in the northern part of HNF, is a good option (although a little further from Louisville), and I hear good things about the Knobstone Trail. I think that there are article son Backpacker.com and Indianapolis Monthly about the KT that might give you some ideas. The KT is fairly challenging, particularly the parts around the southern end (closest to Louisville).

I also recommend that you check the state wildlife websites re hunting dates for either area. If you go in late September you'll miss the main part of the deer hunting season, but there might be a few special dates, or some bow hunting on deer and other species, in late September.

I'm from the Derby City. Red River Gorge might be a little bit of a drive, but it's well worth it. The Gorge does get crowded in the Fall (lots of people from Ohio) but the geology is mind blowing, lots of natural bridges and sheer cliffs. It's really the only good backpacking area in KY IMO. I'd suggest the Swift Camp Creek Loop for sure.

But be careful in the rest of DBNF. Pot growing is intense and patches are guarded with dogs, guns, booby traps, etc.

The best trails near metro Louisville are in Bernheim Forest, however I don't think any overnight is allowed. The scenery is absolutely stunning and some of the trails are pretty long. The Millenium trail is about 14 miles.

The Knobstone might be ok, but the turkey ticks are horrible in Southern Indiana. Be sure to pack a shelter with noseeum if you hike the KT.