Good question, I'm more than a little bit paranoid about this.
Am booking AA85 (dep JFK 1530, arr SFO 1855) to connect to QF74 (dep 2310) - naturally, separate PNR otherwise I wouldn't be concerned. On paper it seems like more than adequate time, but I've been delayed on AA85 at JFK for quite some time in the past (2-3 hours), and would be worried about such a delay eating up into that considerable buffer and missing the baggage check-in cut-off for QF74.
So I guess the questions are - is it worth leaving even more time up our sleeves (would be a factor of several hours more, as there are no other direct flights from JFK in the late afternoon) and, despite the recent announcement from QF, does anyone know if AA at the least still provides interline baggage check-throughs on different PNRs?