As for The Return of the Joker, I believe that came out between seasons 2 and 3 of Batman Beyond, and I have it placed during season 3. It's a bit hard to place because of the flashbacks, which have to be nearly 40 years before the movie and also have to be after the Joker's last appearance in JL's "Wild Cards" -- if not after JLU's "The Greatest Story Never Told," in which Booster Gold refers to the Joker as still at large.
IIRC, Bruce Timm has said that the RotJ flashback are the last thing to happen in the BTAS -> JLU timeframe. Meaning that it all happens *after* JLU...not sure if that includes the Ace/Waller flashback from 'Epilogue', but I imagine so.
Likewise the main story of RotJ is supposed to be the last thing in that time frame (save for 'Epilogue', of course.)
'Mystery of the Batwoman' was I think supposed to take place around season 2 of Justice League (there's mention of weapons shipments to that fake county who's name I forget, the one Vandal Savage takes over?)
I recall Timm saying at the time that they always kept the exact timeline deliberately loose, with everything basically taking place in 'Peanuts' time. So it's really not supposed to withstand close scrutiny. Only rarely did they ever specify a passage of time from previous episodes and those instances were mostly in JLU when they started getting continuity happy and started tying in everything but the kitchen sink.