...and lord knows, I may be thinking of different evil Leaguers...
...but I'm sure the tiny Leaguers are kept in the JLA trophy room in a little glass jar. I remember during one of the "Secret Files" issues during Morrison's run, Zauriel took you on a guided tour through the trophy room, and there was a moment where he introduced tiny JLAers and said, "It's hard not to laugh listening to the threats of what they're going to do to us" or something.
Not sure where the Lois Mini-Mes ended up, though. Atom's harem? No wonder Jean went crazy.