That would be a hard choice! I've lived in Louisville, Lexington, just south of Louisville, and now south of Etown (an hour south of Louisville and an hour north of Bowling Green). I love Louisville and Lexington! My family is in Lexington, so that gives it the edge for me, but we would move back to Louisville in a heartbeat. We still go up to Louisville often (ice skating, the Zoo, the Science Center, shopping at Whole Foods, eating out at ethnic restaurants, concerts, and seeing our herbalist).
My crunchy, media-free, vegan friend in Etown really likes the Montessori school. Her dd went there for preschool, and I think her son will go there soon. For me, that 2 hour drive to Bowling Green for work would put Louisville out of the running. Etown is only 35 - 40 minutes from Louisville. Lots of homeschooling families that I know drive from Etown to Louisville for get-togethers.
The Waldorf School is on the East side of Louisville (Lyndon). Living close to the school would make it easier to get to Lexington, and longer to Bowling Green.
I'm not sure about Farmer's Market in Etown. My dh just said that there is a seasonal Farmer's Market somewhere downtown. We get all of our produce from Amish farmers in Hardin, Hart and Larue Counties (all just south of Etown).
Can you come for a visit? I think it would really hard to make that kind of decision without spending some time in the area.
We really like the Etown area, but we also didn't have to deal with daycare or school choices. The drive from Etown to Lexington and from Etown to Bowling Green is about the same - an hour and 15 minutes. The drive from Etown to Lexington is easier. The Bluegrass Parkway is lightly travelled. I-65 from Etown to Bowling Green is much more heavily travelled. Is your work evenly split between Lexington and Bowling Green? Would it work to live in either of those places?
You've probably already thought of this, but also keep in mind that Louisville, Etown, and Lexington are in the Eastern Time Zone. Bowling Green is on Central time.