Academic Internet Resources on Indonesia:  Exactly this.  A very nice comprehensive site on the country, and it appears to be updated very often.

Indonesia- History:  This is a nice, brief overview of Indonesia.  Provides some information on the importance of the country to the history of world trading.  Unfortunately, the site has not been updated since 1995, and thus does not include the recent upheaval in the government.

Sejarah Indonesia- Indonesian Timeline:  Although not from an academic source, this appears to be accurate.  It is a very long timeline, and provides a huge amount of places to start your research on.  This also helps to keep the things you get from other research into order and perspective.