I visited the Togean islands in 2002 - I arrived in the main town there (Wakai) then got one of the waiting boats to Kadidiri (probably the most popular/accessible island with resorts there). Beautiful place - blue blue water, white sand beaches, lush green jungle and palms. Simple accommodation at the time - electricity very limited, and mandi style bathrooms. But the food was nice, and snorkelling was fun.
Lots of useful info at
http://www.sulawesi-info.com/togianislands.html The place I stayed at was
http://www.kadidiri-paradise.com/
I did my OW course there, so I can't say too much about the diving.. However the B-24 liberty bomber wreck which crash landed in the water was a good dive (machine guns and tyres and propellers and everything still there!), and a trip to Una Una island (active volcano) had lots of fish. I also heard some talk on some good deep wall dives (as a new OW I couldn't do these), like Taipi Wall or something?
Unfortunately, there was a fair amount of bomb fishing going on when I was there - you could hear a 'boom!' while snorkelling almost every day. Also one thing to be careful about is malaria - this is present, so use DEET repellent and tablets..
Even so, a very rich marine environment, and the above water scenery was stunning! A trip to Taipi island is well worth doing. There were also stilt villages where the sea gypsies / Bajo people live.
The best way to get to the Togeans would be from Manado, then either catch a bus (full day travelling) to Gorontalo, or there are now flights from Manado to Gorontalo. Then AFAIK there is a weekly ferry from Gorontalo to Wakai in the Togeans... Personally I would avoid the southern approach via the Poso region if visiting again (i.e Palu > Poso > Ampana), as there is a weird atmosphere after the communal violence in 2000 between the Christian and Muslim communities there. I did this route in 2002 - lots of police/army checkpoints, burnt out houses, etc.
The guy who taught my OW course also worked at Wakatobi - from what I picked up Wakatobi has much better coral (with prices to match!), but the charm of the Togean islands is its isolated, untouched atmosphere, friendly people, beautiful scenery, and the diving is good. Its still the most picture perfect 'desert island' destination I've ever visited (my avatar photo was taken one sunset at Kadidiri!).