Justice Lords first appeared in Justice League Beyond 2.0 #19 (May 2014)
They're first mentioned - and Lord Superman first appears - in issue 18 (April 2014). They are the Batman Beyond counterpart to the Justice Lords, who first appeared (with Lord Superman) in the Justice League episode "A Better World" (November 2003).
The Phantasm first appeared in Batman: Mask of the Phantasm and then first appeared in comics in Batman Beyond 2.0 #25 (July 2014).
Krypto was an alien that first appeared in the Superman: The Animated Series episode "Bizarro's World" (1997) as Bizarro's pet. It later shows up in a containment chamber of sorts in Justice League Beyond #22 or #23 (April or May 2013).
Morgaine Le Fay's Brand was first seen in the New Batman Adventures episode "The Demon Within" (1998) as a means to control The Demon. It was later used in a similar capacity in Justice League Beyond #14 or #15 (November 2012) when Terry McGinnis had become the Demon.
Darkseid's New Look and his invasion of Earth took place in "Destroyer", the Justice League Unlimited series finale (2006). It appeared in flashback in Justice League Beyond #9 (July 2012)
Superman's time as a New God was shown in the Superman: The Animated Series episode "Legacy" (2000), where he was brainwashed into becoming Kal-El, Son of Darkseid. This event was referenced in Justice League Beyond #2 (February 2012)
The Starro incident happened in "The Call" (2000), one of the last episodes of Batman Beyond. It was referenced in Justice League Beyond #2 (February 2012).
Kobra's mind-control device was used in the Batman Beyond episode "Unmasked" (2001) to try to find out who was underneath Batman's mask. It appeared in a different context in Justice League Beyond #3 (March 2012)
The Possible Future Justice League appeared in the Justice League Unlimited episode "Once and Future Thing, pt. 2: Time, Warped" (2005). It is an as-yet-unconfirmed line up for the team, but not impossible. The team, and the time travelling event that led to meeting them, were mentioned in Justice League Beyond #7 (May 2012).