The pantheon. Click for much larger view.
As we see, the Justice League takes up the top shelf, as befitting their status as supreme beings. The order of the seven is taken from Justice League publicity materials, which always order them in this way.
But then, curiously, the Justice Lords (the evil Justice League from an alternate time-stream) are placed on the same shelf, and in the same order (minus Justice Lord Flash [or Reverse Flash], who is not featured as a member of the Justice Lords proper [except for the false Justice Lords generated by the Luthor/Brainiac monster]).
Below the Justice League are the second-tier Leaguers: Plastic Man (a custom job bought on eBay), Vixen (posed below her current boyfriend, Green Lantern) Shining Knight (who should be posed beside Vigilante, who has not yet been acquired), Black Lightning and Isis (two more eBay custom jobs), Robin (Robin? The hell is he doing here?), Atom Smasher (the lone Justice Leaguer who claims Jewishness as part of his identity in this otherwise areligious team), Green Arrow (mysteriously, not posed next to Black Canary), Aquaman (note that the Aquaman posed here is the one without the cape; this is the real Aquaman), Batgirl (partially obscured) (Batgirl?!), Huntress, Atom, Red Tornado, Hawk, Dove, Metamorpho and Zatanna.
(Sam is loath to place one character in front of the other -- they are all equal [on their shelves] to each other. It pained him to place Aquaman in front of Batgirl but he was forced to due to space considerations.)
Then, we have the third-stringers, or supporting characters: Supergirl (whom I would have placed in the second tier), Orion, Black Canary (another second-level hero, imho), Starman, Booster Gold (a third-shelfer, even though he has his own episode of JLU, Elongated Man (yes, the official Elongated Man is trumped by a custom Plastic Man, as he should be), Nightwing (Nightwing?) Steel, Wildcat, Waverider, Dr. Light (that's Dr. Light II, not the rapist of Elongated Man's wife), Aztek, Dr. Fate, Rocket Red, The Creeper.
I do not know what system Sam uses to rank these figures. Black Lightning is a second-shelfer, even though Sam knows very little about him and has not seen him featured on the show, and while he's never seen a Plastic Man comic and he is not featured on any of the Justice League shows, Sam somehow understands that he outranks Elongated Man (comics fans, of course, know that Plastic Man did not begin his life as a DC hero, he was purchased from another publisher; Elongated Man was the pale imitation DC cooked up so they could have their own stretchy guy). Isis has never been featured on the show or even in the tie-in comics; Red Tornado he finds compelling enough to put on the second shelf, even though the character only has the most passing moments on the show. Robin, Nightwing and Batgirl get included, even though they are not part of the League (and are presumably either off with the Teen Titans or guarding Gotham City, dating Bruce Wayne (Batgirl only) (I think) and growing old while waiting for Terry McGuiness to take up the Batman mantle). (And before anyone starts complaining about Robin and Nightwing being featured at the same time, the Robin featured here is Tim Drake, not Dick Grayson.) The Green Lantern Corps (Katma Tui, Kyle Raynor, Arkkis Chummuck, Tomar Re, Kilowog), although they dominate several key episodes, currently reside in a bench on the other side of the room (presumably the bench is the same relative distance from the shelf as Oa is to Earth). Vixen is posed beneath Green Lantern, but Zatanna is not posed beneath Batman, although they have been romantically linked.
The underworld. Click for much larger view.
On the bottom shelf, crammed together, we have the villains, with the most powerful in the center, growing less powerful (or relevant) as we move to the edges. Thus, Lex Luthor, Joker and Brainiac take center stage (with the Very Tall Darkseid, Doomsday and Bane behind), flanked by Poison Ivy, Amazo, Mr. Freeze and the ultra-lame Copperhead to the left, and Catwoman (seated), Sinestro, Two-Face, Bizarro, Harley Quinn (obscured by Bizarro), and the ultra-lame Mirror Master to the right.
Even casual Justice League viewers will note the preponderance of Batman villains here. Strictly speaking, Joker, Bane, Mr. Freeze, Catwoman, Poison Ivy and Harley Quinn shouldn't be here at all (although some of them put in a brief appearance in a couple of episodes). It is, I'm guessing, their overwhelming importance to the Batman/Gotham City mythos that warrant their inclusion in the Legion of Doom.
I cannot explain Poison Ivy's outranking of Amazo. The Amazo character in Justice League is one of the key stories of the whole series, second only to the Justice Lords scenario. We even have two other Amazo figures (one gold and one clear, symbolizing different levels of Amazo's evolution), which have been banished along with the Green Lantern Corps (perhaps for similar thematic reasons -- Amazo does, after all, leave Earth when it has nothing more to offer him). Similarly, I cannot explain why Catwoman is seated; Sam is adamant about this point however and has corrected her posture on more than one occasion. The Joker's distance from Harley can be explained for character reasons (Joker seems to spend half his time distancing himself from Harley) (He's even gotten Bizarro to hold her off).
Reverse Flash, who until recently lived between Harley Quinn and Mirror Master, now mysteriously resides in a box under the desk.