Hi Mark,
I don't know if you've chosen yet but here is my 2ps worth on the places you've listed and my experiences of them. I've listed when I've been because these places change so much and people rave about somewhere and it turns out they went 10 years ago when the place was pristine and you get there and its poop, or they say somewhere isn't so great but then you get there and its recovered/got better. Some of the photos are not as good as others because they are much older and on compact cameras (at least I know I'm getting better!)
Maldives - Direct flight from UK but expensive
Not been.
Bali
I think I should give Bali another chance. We spent some time there in 2008 and I couldn't really get into it. The liberty wreck was nice but i was disappointed with the macro. I think it had been over hyped to me and I was expecting Lembeh style critters. Even the dive guide at scuba serya where we stayed said it used to be better. He said the divers & guides had chased away the life. We still saw loads, just less than I expected. Very easy to get to though. Booked through divequest (who are great btw). We went in October time.
http://www.pbase.com/suzy_walker/bali_2008
Philippines
The only place I've been in the Philippines is Cebu. It was nice but the viz wasn't as good as I was expecting.
http://www.pbase.com/suzy_walker/cebu_underwater
http://www.pbase.com/suzy_walker/cebu
Indonesia
The only other place in Indonesia we've been apart from Bali, Manado & Lembeh which you listed separately is Raja Ampat. We went on an amazing liveaboard. I'd go back but its expensive so I'll have to save up. We stopped at Lembeh on the way to break up the journey a bit.
http://www.pbase.com/suzy_walker/raja_ampat_mangroves
http://www.pbase.com/suzy_walker/raja_ampat_indonesia_2009
Manado
I flooded my camera in Lembeh and we had two days in Tasik Ria with only a disposable compact, I didn't miss much. We could see the fishermen next door loading up all the fish but I didn't see many underwater! This was in 2007. I was told by another guest that 5 years previously the place was excellent but not sadly not since they'd over fished. Its not on my list to rush back to.
http://www.pbase.com/suzy_walker/indonesia
Lembeh – love it! love it! love it! We've stayed at Lembeh resort twice now. Amazing critters & great food & dive guides. It is a bit of a trek to get there though. Flight to Singapore them a flight to Manado then a car then a small boat across the strait. Worth it though. We went Feb & March time. We'll be going back again I'm sure.
http://www.pbase.com/suzy_walker/lembeh_strait
http://www.pbase.com/suzy_walker/lembeh_st..._indonesia_2009
Bonaire - 2 flights from UK - direct from Amsterdam
I personally didn't rate Bonaire, but I know many ppl who love it. I found the colours very bland compared to the red sea. However, I might be bias and I've seen some amazing photos from there from the people who went on boat dives. I don't particularly like shore diving (you get your legs bashed by rocks and there are always urchins, why are there always urchins?) but the driving around in a truck was cool and the kitting up on the road and wading into the harbour by the boats with people giving you odd looks were cool. We didn't do as many dives as I'd have liked (because we could not seem to self motivate between us). We didn't dive with a guide but still managed to find a seahorse. This was five years ago so it may have changed. We stayed at buddy dive which was nice enough, but you had to go next door to capt dons for dinner though. We went November time. I might give it another chance one day but there are many more places to get to first.
http://www.pbase.com/suzy_walker/bonaire
Thailand:
We went to Koh Tao in April 2006. It was a nice place and I enjoyed the diving but the viz was very poor. My bf got so bored with the viz that we did a rescue course! But it was good fun and the people in the dive shop were great. We stayed at the Koh Tao Cabana (which was more expensive that other places buy very nice) and dived with Scuba Junction.
http://www.pbase.com/suzy_walker/thailand_underwater
http://www.pbase.com/suzy_walker/thailand_koh_tao
Another place you might want to consider is Cayman...
http://www.pbase.com/suzy_walker/cayman2010
We went this yeah for Alex Mustards trip in Jan and it was lots of fun. The food was very expensive though.
I'm actually hunting for places to go this year and next – happy shopping.
Suzy