Any D20 games in which magic has bad side effects?

[JustaPlayer]

Sovereign Stone has side effects. It's a skills based magic system though.

 

[ruleslawyer]

Iron Heroes has substantial side effects, including misfires, backlash, and flat-out spell failure. Moreover, the fanbase has created an even more elaborate set of house rules for spellcasting mishaps. Mastering Iron Heroes (the IH "DMG") has rules for magic item flaws and curses as well.