Batu Caves just outside of KL are meant to be ok and worth a visit if you're in the area.
Other stuff i know about is somewhere just outside Kucing (Bat Caves i think) and some stuff on Kinabalu - both on Borneo Island
Other than that I'm in the dark - there is a guidebook for Singapore and Malaysia which had quite a bit of stuff in it, lots of big limestone faces, but i think the majority are still largely undeveloped.
