Hi,
I live in Bali for the last 10 months working as a dive instructor. Strictly talking about the diving, this is my opinion:
- Menjangan: probably the best coral in the island: great variety & very healthy. This is my first option about diving in Bali. Coral and small stuff is the best (electric clam, orangutan crab...), although you can see some bigger things like black tip & white tip shark, turtle and occasional manta, mola and whale shark (a couple of them spotted last month!).
The night dive in Bajul Bay is great too. If you are into muck diving, close to Menjangan it is the Secret Bay in Gilimanuk, you can find there what is rare in other dive sites (ghost pipe fish, fingered dragonet, frog fish), very good for photographers.
- Nusa Penida: this is the place to go if you want to see Mantas (in Manta Point or Manta Bay). Crystal Bay is popular for the Mola Mola, although is harder to see than it used to be. Water is colder than in other places in Bali, and Penida is famous for the strong and changing currents. So don't go with a cheap dive center you can't trust, please. On the north and in Lembongan there's many drift dives. Blue Corner is a place particularly famous for being risky to dive, don't go there if you are not confident with strong currents. Reef hook advisable.
- Tulamben: it's a great place to dive. The Liberty Wreck itself it quite a wreck, I mean don't expect to see the ship in good condition. The dive, is very good though. Besides the wreck, you have a couple of dive sites close to it life Coral Garden (very shallow and beautiful) and Drop-Off (wall dive).
- Padang Bai: it is good for a day. The jetty is particularly nice with a lot of marine life underneath. Blue Lagoon is not as good, but you have good chances to see cuttlefish (which I love!).
- Amed: I dived only a couple of times, and I didn't really liked it. But some people I know they love it, so I couldn't say it's bad or good.
Make sure you dive with a reliable dive center. It's not worthy to save some bucks, and discover that your guide is OW, there's no O2 in the boat, etc... it happens, believe me.
If I can help you with anything, please PM and I'll do my best to help.
Cheers!