I like
Nudi Falls as it has a bit of everything. a mini-wall with soft coral and a shallow bottom. Good for night dives.
You can see a map here for Lembeh
Dive Lembeh with Two Fish Divers - dive Lembeh Straits, muck diving capital of the world
The dive operators have an understanding in the Bunaken and Lembeh areas, no more than three dive boats at one site.
Most sites are just a few minutes away if you are staying in the more central area of the mainland or Lembeh Island.
Night dives are great fun in Lembeh. Do as many as you can.
Be sure to ask your dive operator about Diver to Guide ratios and whether they have any time limits on the dives. The less divers per guide, the better. Four or Three to one is typical of the better dive operations, sometimes if is just one guide to one diver.Tell your guide what you want to see and they will find it for you in most cases.
Bring a small light for using in the day time as a back up at night (if you are going to be using the dive operators primary light).
Don't forget your International Departure Tax if flying out of Manado back to Singapore. It was 75,000 Indonesian Rupiah (about US$8) in April 2007. Payable in Rupiah at a counter after you check your luggage and get boarding passes, before going up the stairs to the departure lounge. Verify the current amount when you arrive. I don't know what it is domestically and for international departures at other airports.
If flying on back to Singapore on Silk Air and then connecting to a Singapore Air flight, you will probably be getting assigned seats and boarding passes (sometimes their printer is down and you will have to get the actual pass at one of the transit counters in Singapore airport) it is worth visiting one of the transit counters anyway, and asking if you can a seat with better leg room. Certain seats are blocked and only released if not needed a few hours before the flight and may have extra leg room.
I was able to get a seat that normally are held for persons traveling with infants and the seats face a wall with special connectors for mounting the crib on the wall so there is extra leg room on the Boeing 747, plus no one pushing their seat back into your face and the video screen comes out of the seat and is on a long articulated arm that you can set just right for viewing.
So remember to ask.
Also when flying a large plane like a 747, if you order a special meal you will get served first. Singapore Airlines offers a large variety of both vegetarian and non-veg meals which can be ordered online.