I found no problems in Indonesia and malaysia, nether did any of the MANY people i met there from many western countries. that being said, Malaysia is a very muslim country and Indonesia has militant rebel groups on some islands (especially bande Acheh) I met a german girl working as a Aupair(sp?) there and she LOVED it but felt a bit nervous jogging around the football field and seeing paramilitary forces drilling in bandanas for eventual rebellion against government – ever since East Timor wom independance after 30 year struggle against indonesian central government- other extremist groups are encouraged to keep fighting – it is a huge nation with widely varied ethnicies not all at peace with central government and may be a failing state that could collapse, just like yugoslavia… HOWEVER… BVali is very safe EXCEPT for terrorism which you are just about equally at risk for in paris london madrid or new york, right? the people there are peaceful loving hindus and so kind and harmless, but as a tourist place it was targeted twice by rebel groups from OUTSIDE of Bali.
Malaysia is not homogenous, but as far as i know is safer than the rest of indonesia as it has less rebel groups and a strong agreeable central government (especially within peninsular malaysia. Borneo may be more sketchy)
so your experience may vary, and Jakarta for example is rough around the edges in some places, however i never felt unsafe and I enjoyed Malaysia and Indonesia. Bali is the cream of the crop, the best of the best, and if you are there, i would recommend (and so would all my friends who were also there) that you see other parts of southeast asia as well, do not rule out eastern and western Indonesia, just skip Acheh! My friends LOVED Flores and Komodo. I wish i had time to go there. Java was nice, but more sketchy than, say, Thailand which has more tourist development. nonetheless when a bus dropped me off at midnight on the side of the road in the middle of nowhere in Java (it was very late) we were able to get a taxi to a hotel and then late the next day get a bus to hike a volcano and we never felt unsafe or threatened.