As Jeff mention, there is preflight in InDesign, as you know. This is great for many cases. That said, many also opt for the stand-alone option of FlightCheck. Like this book/advertising customer:
FlightCheck user review from Terri Wright, preflight for prepress for book printing - YouTube
The point is with FlightCheck, is that it often goes deeper, especially with embedded elements within placed EPS, AI or PDF files.Watch: InDesign vs FlightCheck - Round 1 - Placed PDF Problems - YouTube
And it checks many file formats other than just InDesign.
Friendly Regards,
David Dilling
Markzware(Makers of FlightCheck)