Innately Evil/Good Spells or Powers:
If he is a Divine spellcaster, his deity may punish him (DM's choice) depending on the situation of the spellcasting.
Arcane casters have a greater leeway but evil/good acts against one's alignment may shift your alignment towards the other end. Also, the spellcaster must remember he does not function in a vaccuum, and his companions may not like the results of the spells he casts.
Psionic powers rarely have an alignment associated with them but acting against one's alignment can be psychically unnerving and can cause loss of powers or power points (DM discretion).