Here's a list that I made(in alphabetical order,with reasons) that might give Superman some trouble:
Apocalypse-turns the atoms of his body into kryptonite
Asylum-teleports supes into darkforce
Basilisk-manipulates molecules around supes and turns them into kryptonite
Blind Faith-takes mental control of supes
Blockbuster-strong enough to fight with Thor
Jamie Braddock-can alter reality
Cable-destroyed silver surfer's board
Chrome-transmutes area around supes to kryptonite
Copycat-makes a exact copy of supes to fight the original supes
Darkstar-same as asylum
Darwin-reactive evolution lets him adapt to all of supes powers
Dirtnap-takes over supes body
Elixir-turns supes body into kryptonite
Empath-makes supes depressed and want to kill himself
Emplate-steals supes powers
Exodus-possesses high psionic powers
Fantomex-strong,heals,and can trick even the best telepaths
Franklin Richards-reality manipulation
Gamesmaster-manipulates supes thoughts to kill himself
Gideon-mimics supes powers
Holocaust-can drain supes lifeforce
Karma-takes over supes brain
Lifeguard-her body adapts to supes powers
Mad Jim Jaspers-bends reality
Mr.Immortal-he is immortal