I too was shocked at the price of rt SIN-MDC in June 2007. I was looking it up when I booked my trip in fall 2006 and the price was $1154 SG back then. It went down to $500SG ($380ish USD) when I did the actual booking on Silkair.com in April 2007. The websites seem to only offer full fare Y tickets far out from the actual date, and lower the price (by changing the Fare class to lower fare classes) as you get closer to the date of travel. Sort of the opposite of that in the US.
Yeah, it is expensive to go on Silkair, but it makes up for it with only a 3 hour adventure rather than >9 hours on Garuda from SIN, or on other airlines that are difficult to book via the web.
Have a great trip, however you get to Manado.