Looks like I am late to the party. I lived in Manila for nearly 20 years and had a house in Anilao, and like others have dived all the locations mentioned. There is lots of good info here already but I will chime in anyway for future reference.
(Tim / Chris / Davide / Rich: maybe a travel forum with one thread per destination would be a good way to document the collective wisdom of the group?)
General info on Philippines destinations
As for diving here, I can't say enough good things about it. There is much info online so I won't try to summarise beyond this: Anilao is a great macro destination that also has a few decent walls, but no pelagics to speak of. Further afield, diving in Puerto Galera, Bohol, Dumaguete and Apo Island are much the same as Anilao while Malapascua and Moalboal are great for sharks and turtles. Coron has wrecks. Cebu is overcrowded in my opinion. Tubbataha is a magic place with beautiful drift diving along huge walls passing through schools of barracuda, eagle and manta rays, tuna, sharks, and the occasional whale shark, it's liveaboard only, but well worth the effort.
For those who want to see more than one area, be aware that moving around the Philippines is a huge pain in the neck and will always take all day no matter what anyone promises. If I had only a two week trip, I'd go to Anilao and either Bohol or Malapascua. I would not try to go three places as the transfer days would ruin my vibe.
Resorts are available at all prices and qualities, and diving is just about the cheapest in the world. For those with non-diving partners, I do not know of a single resort that combines diving and photography, plus spa and high quality food. It seems to be one or the other.
In most places, three or four dives a day would be considered standard, and night dives are easy and affordable. Arranging a private boat for two divers with a guide is in the range of $75-100 per dive total at Anilao and PG if you're staying a number of days and are a good negotiator.
The best time of year is November - March when the water and air are a bit cooler and the vis a bit better. July - October (+/-) is typhoon season and unpredictable. You might get lucky or unlucky. Avoid at all costs the Christmas and Easter holidays, everything including dive sites get overcrowded and noisy.
i'm a big fan of Anilao for macro for sure, where every site is target rich. There are three or four sites where you can get consistent WA shots and another three or four where you can get lucky with WA sometimes, of course a couple dozen sites for macro, and one or two fun drift dives. A big advantage is that if the weather turns, you can still get to good sites with slightly longer and bumpier rides. Depending on your approach to travel, an advantage or disadvantage is that, once back on dry land, you are limited to your resort - there is no town and no nightlife, and at most resorts you can't even walk to the nearest neighbour - it is a very quiet and relaxed destination.
PG is pretty much the same diving as Anilao, as they share the same ecosystem across the strait. To be honest, from an UW perspective, I see little point in doing both unless you are a tech diver as that scene is very big there. The only real differentiation is that PG has a town in Sabang you can walk to from most resorts. So you have a choice of bars and restaurants (all fairly average), and a small strand were you can buy a few things and have a coffee or a beer on the waterfront. Just be aware that it turns into a very "adult" scene at night where many places are not so family-friendly.
Should you decide to go to both Anilao and PG, you can easily find a boat that will do it by private arrangement (there is no scheduled ferry). A major advantage of that plan would be a dive or two at Verde Island, which is a bit too far for a normal day trip but perfectly sensible if transiting from Anilao to PG or vice versa. Arriving at Manila, it's a 2.5 to 3 hour drive to either Anilao or the pier for the 90 minute ferry to PG. Your resort will most likely arrange the transfer by minivan. Neither should be attempted after dark - please believe me on that point.
Bohol has easily the "beachiest" resorts, with lots of white sand, lovely resorts with nighttime massage pavillions, great day trips and island hopping, and a quaint strand when you aren't underwater. Plus you can see tarsiers! Diving is very similar to Anilao and PG.
Malapascua is totally different. It's tiny, and a step above basic, but the thresher shark diving is great (though at the start you're in dark water at 30m at 0500). The dive centers can also arrange a pre-dawn trip out to a seamount where there are often hammerheads. There is a small reef and a mandarin fish dive for evenings (as there is also in the others).
Anilao - UW photo centric resorts
There are resorts at every price point. Food is generally good but not gourmet quality, rooms are generally well above basic but short of luxury.
Acacia: Lovely terrace and pool and outdoor dining, and the best photo and gear rooms I've seen anywhere. Small but AC rooms. Quality is upscale for the area. No good shore diving. Owned and operated by a photog
Club Ocellaris: Haven't stayed there, but gets raves from local and international visitors for their dive and photo ops.
Crystal Blue Resort: One of the better known, has a resident photo pro, the "go-to" place for local UW photogs. Small resort. OK shore diving. They regularly run blackwater dives now.
Buceo Anilao: The newest in the area, run by European partners, attracts keen photogs. Larger than average rooms, good shore diving.
Anilao - dive centric resorts (yes there are some that are not!)
Dive Solana: The most tropical feeling resort in the area. One of the few with a halfway useable beach. Very solid dive ops, photog friendly. Rooms a bit bigger than average, decent quality. Good shore diving.
Altamare: Same evaluation as Solana, a lot newer and somewhat nicer. Also on the beach. Used to be named El Pinoy, you will find more online using the old name.
Dive Planet: Very popular among local divers, can get a bit busy. Haven't seen the rooms but hear they are a bit basic. Famous for unlimited shore diving at the site Twin Rocks.
Anilao - upscale places that can arrange diving
We know these from friends who go for relaxing beach weekends and rave about things like peace and quiet and spa services. All are a bit more upscale and can arrange full dive services but that is not their primary business, which may or may not appeal to hard-core divers.
Aiyanar; La Chevrerie; Awari Bay; Casita Ysabel, Vivere Azure: Of these, Aiyanar and La Chevrerie are the only two that I have ever heard great reviews of the food. They are not dive resorts, so you would want to talk to them first about whether they could accommodate through a private boat and take care of gear properly. Casita Ysabel has the best spa services, though still pretty basic.
Avoid Sea Spring Resort like the plague - it has a big presence on the web but is too big, crowded, noisy, and not very well maintained.
Puerto Galera
Out of the Blue Resort has a very good dive op, a great restaurant (something not very common at any dive destination in the country), and best of all has a 2-bedroom suite at the top with a full kitchen, lounge, and fabulous terrace for about the price of a nice room elsewhere. It is also just a bit around the bend from the night-time frenzy in Sabang but still quite walkable when you want some nightlife. There are good restaurants and bars in Sabang but beware there are also more than a few that are not family appropriate.
El Galleon / Asia Divers is the best known but it is very busy and smack in the middle of the path of everyone walking to and from Sabang at all hours of the day and night.
Atlantis is very well know but it is in the middle of Sabang, not on the beach, so I would not want to holiday there.
La Laguna Villas is popular but not diver-centric.
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Malapascua
Tepanee is very nice with lovely shady terraces and a pool, and a pretty good restaurant. I prefer Evolution though - it is a bit more basic but runs easily the better dive operation. Both have great beaches.