There's basically three worthwhile options for non-flying weekend diving from Manila - Anilao, PG and Subic.
The sites depend on what type of diving you are looking for but my thoughts would be Anilao has the best diving, PG has good diving and great night life while Subic has some very good wrecks and okay nightlife but offers less in the way non-wreck diving.
If you have access or can hire a car then Anilao can be from less than two hours to more than 5 hours away depending on traffic! Most weekend trips will take 2.5-3 hours from Manila but leaving at 5am take half an hour of the journey while leaving after 8am normally adds an hour! The PG route is the same as Anilao up to the end of the Star Tollway so same conditions apply - it's normally about 2 - 2.5 hours to the port then another hour for the boat transfer.
Subic depends on where you are in Manila, from northern Manila / QC it's easy to get there in 2 hours as it's a short distance to the North Express way. From South Manila it's a much longer trip as you can spend up to 2 hours on EDSA if you're unlucky and hit the weekend traffic! Make sure you leave early if you're staying in South Manila and you can still make it in 2 to 2.5 hours.
The same logic applies for travelling from North Manila to Anilao/PG, although normally the morning traffic seems worse going north on EDSA than that going South - I've only done the early morning North to South Manila on EDSA two or three times though so can say for sure!
My advice would be Anilao as a first priority, excellent diving but not much to do outside of diving - no problem for weekend trips though! I'd recommend Arthur's Place but if you're diving alone maybe Aquaventure or Planet Dive would be better as there is likely to be more groups to join to keep boat costs down.
If you get a second weekend, or would prefer wreck diving, then Subic is well worth a trip - There's already plenty of advice on where to stay and how to get there above
PG is a good place to visit but if you only have weekends I'd put Subic and Anilao above on the priority list. If you can get a long weekend through public holidays, annual leave, sudden sick day from work etc. then it's worth going - if not then the logistics of getting there are a pain or very expensive if you get private transfers.