One of the best 90s JLA stories is 'Tower of Babel'. In this story, Batman's contingency plans against his fellow Justice League members are stolen and used against them. It shows the complex relationships within the team and the potential dangers of over - preparedness. Another great one is 'The Great Darkness Saga'. It involves Darkseid and his schemes, with the JLA having to fight against his powerful forces. This story really showcases the scale of the threats the JLA faced in the 90s.
The 'Rock of Ages' storyline is among the top 90s JLA stories. It has a great mix of action and moral dilemmas for the Justice League. Lex Luthor plays a major role in this one, and his plans to take down the JLA are quite elaborate. Also, 'JLA: A League of One' is a really good story. It focuses on Wonder Woman's journey as she takes on a threat alone that she believes the entire JLA couldn't handle, highlighting her strength and determination.
Well, 'No Man's Land' is a very important 90s JLA - related story. It's more about Gotham City, but the JLA has some involvement. It shows how the city descends into chaos and how the heroes respond. Another one could be 'JLA: Year One' which details the early days of the Justice League in the 90s. It gives a good look at how the team was formed and the challenges they faced at the very beginning.