The JLU episodes were made after Beyond, and seem to reference things that happen later than the series ever showed. This is the order that seems good to me, from Batman to JLU (Just started watching it all a few weeks ago, currently in Superman vol. 1)
Batman TAS volumes 1-3
Mask fo the Phantasm (seems like it might take place earlier, but its not important continuity-wise)
Sub Zero (takes place after "Deep Freeze" in volume 3 but before the Mr. Freeze episode in Vol. 4)
Superman TAS volumes 1-3
Batman TAS volume 4 (the Gotham Knights episodes)
Batman Beyond
Return of the Joker
Justice League volumes 1-2
Justice League Unlimited Volumes 1-2
The volume numbers are how the DVD sets break down. also you could throw in Batman: Mystery of the Batwoman, and the superman brainiac movie, they'll probably fit anywhere after their respective series.