Pelni : public inter-province ferry transportation, with prices and reliable schedules
ASDP : public within-province ferry transportation, with prices and unreliable schedule
The article about boat travel in Indonesia will probably be a useful complement
Tiket.com : a private website acting a 3rd party re-seller for plane and train tickets. Efficient and good customer service. Traveloka is one of the reliable alternatives.
Wild Sumatra : a local eco-tourism agency based in Sungai Penuh, offering trips to Jambi and Bengkulu provinces. Run by passionated Luke Mackin. Tons of information and pictures, great both for those looking for a tour guide as well as independent traveler.
Mentawai.org : plenty of information about traditional Mentawai culture
Bali and Nusa Tenggara
Kalender Bali Digital : an online Balinese calendar giving you all the ritual special days and ceremonies (in Indonesian).