I have dived in many places including Thailand (amazing diving) and while I haven't dived Bali yet, I hear only amazing things. I did in fact Dive Indonesia in September 2008 as I went there for my honeymoon. Well actually we went to a magical place called "Wakatobi". It is located a 2.5 hour charter flight from Bali. They say that this place has the best house reef in the world! - And it does! The wall diving was spectacular! An all inclusive week will set you back approx $2100US, but hey, if its as good as the reviews, its just a drop in the ocean so to say. By the way, I live in Far Nth Qld on the Great Barrier Reef so I guess that's saying something.
Amazing places I have heard about in Bali include;
Tulamben - USS Liberty wreck (no currents easy dive 5m-30m)
Menjangan Island - National Park (day trip from Kuta)
Blue Lagoon (Sharks!)
Nusa Lembongan / Nusa Penida
I will post an update about this once I have dived these sites.