Hro Talak is not quite Katar Hol, but his name is an anagram and he was also given a past relationship with Hawkgirl.
Galatea is not exactly Power Girl, but she wears a similar costume, which one scene made identical with the addition of a red "towel" hanging over her shoulder, and shares the background of "not exactly Supergirl, but close."
In the same episode, the screaming minions that the heroes fight in Ichthultu's world are clearly based on Marvel's Mindless Ones, and Ichthultu himself is based on Cthulhu.
The Justice Lords from "A Better World" were heavily inspired by The Authority, which the producers had begun to read between seasons one and two, and one idea they had was to see what the world would be like if the League ever tried to emulate their tactics.
When Brainthor summons up robot versions of the Justice Lords to distract the League, he has to create a new one for Flash (since Flash of that universe died before they became the Lords). The costume he gives Flash is identical to the costume of famed Flash Villain Professor Zoom, The Reverse-Flash.
The giant turtle that attacks Japan in "Chaos at the Earth's Core" is an expy of Gamera, as well as being a Mythology Gag to Jimmy Olsen's comic book.
Ace is one to Tamara. Both are young girls with black hair and powerful psychic abilities and were use by shady organization and are also associated with a Batman.
The Justice Guild of America was a very thinly-veiled Expy of the Justice Society of America, with Green Guardsman standing in for the original Green Lantern, the Streak for the Flash, Catman for Wildcat and Black Siren for Black Canary. The exception was Tom Turbine, who was instead based on Dynamo of the T.H.U.N.D.E.R. Agents. The group's Tagalong Kid, Ray Thompson, was based on comic writer Roy Thomas, who is known for his love of Golden Age superheroes. Their two-part story arc was an adaptation of the first JLA/JSA team-up story set in an Adam West-styleWorld of Ham. This was done mostly because DC wouldn't allow them to use the actual JSA as was planned, thinking that a story presenting the JSA in the goofy (and slightly racist and sexist) style that that episode did would shine badly on the recently relaunched JSA comic series. It worked out well for the producers, though, as they were able to use some of the JSA the characters legitimately in Justice League Unlimited.
The villains of the episode were themselves Expies of The Wizard ("Sir Swami"), Icicle ("Doctor Blizzard"), Sportsmaster ("Sportsman"), and The Fiddler ("Music Master").
The beginning of the episode had the League fighting a giant robot that looked just like an Evangelion with the serial numbers filed off. It's face also resembled that of Ultron.
Wade Eiling becomes an Expy of the Hulk by using the Captain Nazi serum. He's more articulate but possibly even more dangerous due to being a Principles Zealot.
Similarly, the Ultimen are expies of the Superfriends original characters, the Wonder Twins, Black Vulcan, Apache Chief and Samurai.
The entire episode was a homage to Super Friends; the Ultimen base on top of the skyscraper looking like the Hall of Justice, Long Shadow's cell ringtone being the old theme, even how they only used Superman, Batman, Aquaman, and Wonder Woman as the hero team in the episode.
There's also Devil Ray, who is basically Black Manta with a name change. His rivalry with Aquaman is never mentioned (due in part to the rights for the character being held up by the WB's plan for a Smallville style show focusing on him), instead being matched up against Wonder Woman for most of his appearances.
Solomon Grundy gains quit a bit of the Hulk's characterization.
The Annihilator from "Hawk and Dove" is suspiciously similar to the Destroyer from the Thor comics, being a nearly-indestructible suit of sentient armor forged by a god. Even the name is similar.
