Lower spell DC's for anyone whose casting stat is Intelligence.
Loss of both bonus spell slots and ability to cast high-level spells for the same casters. (Not sure which of these you meant in your post).
Loss of access to high-level metacreative psionic powers.
Loss (as far as I can tell, since the stat will suddenly not have been stable for 24 hours) of bonus psi points for Shapers.
Lower Intelligence modifier for all purposes (which includes, but is not limited to, Intelligence based skills as you mention).
Loss of conscious thought if the stat drops to 0.
That pretty much covers it. What kind of penalty were you thinking of?