I just got back this Monday from spending 3 weeks in N. Sulawesi.
I went with a low cost operator SDQ. It's the opposite of Lembeh Resort and KKB. But for $75 per day including bungalow, meals, and 3 dives per day, you can't beat it. I was fortunate to be the only guest in the whole resort for half my stay. That meant that I had a personal dive guide. Ask for Rudy if you use them, he's been diving the area for about 20 years and will find what you want. For Lembeh, having a great guide is important.
Must do Dive sites that I would do with my wife:
#1. Nudi Retreat - this is the place to shoot pygmies as you will find them at about 40-50 feet. 20 yards from the cave, in 15 feet of water are extremely tiny white pygmy seahorses. There were enough loaded seafans, that many photographers could shoot at the same time. also loaded with nudis. Inside the cave are electric rocks (clams). I ended up doing this dive 4 times.
#2. Pante Parigi - on one dive I got a hairy frogfish, large seahorses, white bearded frogfish and then at the end of the dive there is a cluster of some of the most beautiful coral I've seen. This site is problably less visited because it's probably not considered one of the popular ones. This was actually one of my favorites and I discovered it on one of my last dives.
#3. Hairball 1 & 2 - hairy frogfish, different pipefish, and an assortment of scorpionfish
#4. Nudi Falls - popular. nice for night dives.
#5. Mikawade 2 - clown frogfish
#6. Angel Window - beautiful and loaded with different stuff.
#7. actually, all the dives are good. some sites you might muck dive for half hour and not see anything, and then, bingo. other sites, you might drop in and find 3 different frogfish in front of you.
Topside, stop by the zoo. It's basically somebody's backyard, but there's neat stuff there and in 15 minutes and for 2 bucks it's worth it. They have a 200KG python if you want to see a big snake.
Prices are ridiculous. Before going to the resort I stopped at the big grocery store and spent 10 bucks and got 8 bottles of water, 7 packs of cigs, 5 boxes of mosquito coils, and a bunch of candy.
I booked my air tickets directly with Singapore Airlines. It was the best deal that I found and for $700 3 days before departure, I'd say that's pretty good. I took SilkAir from Singapore to Manado at about $370. I had 100 pounds of luggage and 50 pounds in two backpacks. The limit is 30KG checked in. They dinged me $127 on the way there and gave me a freebee on the way back. There are other carriers, so next time I would do more research.