JLA: Superman (Needed), Batman (Probably quite easily killed), Flash (dead), Martian Manhunter (Possibly needed), Wonder Woman (Needed), Green Lantern (Depending on the incarnation, needed).
X-Men: Cyclops (Probably killed fairly easily by Thanos or Darkseid), Jean Gray (Needed if she's in Phoenix mode), Beast (Dead), Wolverine (Dead or at least incapacitated), Storm (Last a while, essentially dead meat).
That's the X-Men power players there, all but 2 are needed effectively.
Avengers: Thor (Critical), Iron-Man (Needed), Captain America (I'd love him Dead but he's needed), Vision (Depending if he's included, Needed.)
So all in all the sides would look like this:
Supes, Wonder Woman, Manhunter (maybe), GL (maybe), Cyclops, Jean/Phoenix and the whole team of Avengers.
Now given that there are alot more members of the X-Men and a few more in the Justice League, you could argue that the numbers would be too much. You really have to take into account just how powerful Thanos, Darkseid and Apocalypse will be combined. The X-Men have trouble with Apocalypse, or HAD, for the better part of the time he's been in the comics, Thanos has God like power with or without any additional item and Darkseid the same. It's a safe bet that The X-Men are gonna be the first team out of there, possibly in pieces. The Avengers are the best team there and the difference maker for sure. While they have no Superman, they have Thor who I think could give Supes a run for it any day of the week. But even then, could the Avengers and the JLA REALLY make the win happen?
-AC
ok.
I think the good guys would probably take it. I mean Superman alone can go toe to toe with Darkseid. Let him have the JLA to give Darkseid a Challenge. Avengers take on Thanos, wich will be very hard for the heroes but they most deffinatley can do it. And leave Apacolypse for the Xmen. The bad guys seem to be far out numbered.