All in all, thanks to the close historical and social ties between these two countries, the relations between them remain essentially quite cordial as far as I know despite some of the problematic issues that Cahaya raises in her post. If asked, I would think most Malaysians, regardless of their ethnic background, would see Singapore as their closest friend and ally (correct me if I am wrong Cahaya) and the Singaporeans would probably have the same feelings about their Malaysian cousins (Snowybeagle, if you see this thread, correct me if I am wrong). I would even think that Malaysians in general may have a more positive perception of Singapore than Indonesia. I would characterize the relation between the two countries a symbiotic one, one that benefits both.
Having said that, like between any two neighbours or even between two siblings, disputes and occasional quarrels are inevitable.
On one hand, I think some Singaporeans may have a rather condescending attitude towards Malaysia even though the very survival of Singapore, a country entirely without natural resources, is dependent on Malaysia. Such an attitude (which is not directed just to Malaysia but to its much less wealthy neighbours too) is the almost inevitable consequence of long-term prosperity of this city state. When you realize that the income discrepancy between you and everyone around you is so huge, it takes a lot NOT to act in an arrogant manner.
On the other hand, exactly because of this discrepancy in wealth and standard of living, even though Malaysia is not poor, some Malaysians must eye the Singaporeans with a sense of envy or jealousy. After all, Singapore could have well been a Malaysian city if history had not turned out the way it did. (Actually one could also ask the question of, "What if Singapore had stayed within the Malaysian Federation. Would it have been able to achieve what it has achieved today?")
One also has to remember that Singapore left the Malaysian Federation in 1965 not exactly on the most friendly terms. Singapore was expelled from the Federation after heated ideological conflict with the Federal Government in Kuala Lumpur. I wonder if some Singaporeans still bear a grudge against that.