Indonesian Recommendations

Bali (all in Ubud)

Honeymoon Guest House - a bit more expensive than a backpackers budget but still very reasonable with great breakfast and a nice pool area
Gusti Garden Bungalows - a cheaper hotel in Ubud which was still very nice
Sedona Spa - $8 massages in a beautifully clean and comfortable spa... Not bad.

Kalimantan
Borneo Expeditions - Organizes multi-day trips into Tanjung Putting National Park to see the Orangatuns. You pay a bit of a premium to book through them (versus spending a day hunting for a boat and guide down at the dock) but Danson, the guy in charge is extremely responsible and organized. He can also book your flights for you which proves invaluable if you don't speak Indonesian.

Flores
Reefseekers - an EXCELLENT dive shop for exploring Komodo National Park. We dove two days with Kath. It had been awhile since either of us had dove and she made us feel completely at ease, even with the currents that Komodo is famous for. She was incredibly knowledgable about the sea life and we loved the briefings before each dive. They are building upscale bungalows on an island in the area and we're already planning our next trip to Indonesia around returning to visit :)

Lombok (Kuta)

Surfer's Inn - is a great place to stay even if you're not a surfer (although, warning, you will be subjected to endless hours of surf videos at the bar and strange looks as you head off to the beach without your board in tow).
Ashtari Restaurant - an amazing vegetarian restaurant perched in the hills above Kuta. You'll need a motorbike to get there.

Lombok (Gili Air)
Blue Bar - Dean, the owner, is great. Wonderful sunset views.
Italian Restaurant - We can't remember the name but it's the only Italian restaurant on the island, recently opened (as of March 2009) and run by Italians who make their own pasta. It was a delicious break from Indonesian cuisine.

Sumatra (Danau Toba)
Samosir Cottages. We visited many of the hotels in town before settling on this one. Great swimming area and rooms
Jenny's Restaurant. Delicious food (especially the beef rendang) and Jenny was so nice.

Sumatra (Pulau Weh)
Norma's. Best place to stay and eat in Iboah. Norma and the rest of the folks there are a real treat to be around.