This is something I've never had to do -- not in a decade of shooting/using MiniDV for myself, for family, for friends, and for clients. So I'm not immediately aware of existing software that does this, including software I already own (Adobe Premiere Pro,
Sony Vegas Video, Final Cut Pro, Pinnacle Studio, etc).
A quick Google search shows several options:
vDTS (Visual DV Time Stamp) is older, and I see people recommending it online at several sites: tomshardware, creativecow, videohelp.
Ulead Video Edit Studio, a discontinued software, also appears to have had the function built-in.