ORIGINAL: Jajusha
As per the manual, in the full 43-45 campaign you have 3 separate VP counters tied to the allied Strat bombing:
1) Axis industry
2) U-boat factories
3) V-bomb sites
Point 2) and 3) are tied to the date your in.
On 43, the game keeps track of how many u-boat factories there are, and how much you damage, and gives you a VP penalty for the amount of u-boat factories not damaged at the end of each turn. Meaning, if you bomb 100% of the u-boat factories, you get a 0 penalty per turn.
On 44 and 45, the game STOPS keeping track of u-boat factories, and starts keeping track of V-bomb sites and factories, using the same system as per the u-boats.
Point 1 is a bit more tricky.
The axis industry is divided in 5 categories:
1)German Manpower
2)German Heavy Industry
3)Axis Oil Factories
4)Axis Fuel Factories
5)Axis Synthetic Fuel Factories
So, bombing, per example, a french armaments factory nets you absolutely 0 VPs.
Now, onto more detail. There are a total of 8202 factories that go into those last 5 categories.
1)German Manpower - 5973 points, totaling 72.8%
2)German Heavy Industry - 1392 points, totaling 17%
3)Axis Oil Factories - 260 points, totaling 3.2%
4)Axis Fuel Factories - 332 points, totaling 4%
5)Axis Synthetic Fuel Factories - 245 points, totaling 3%
With these numbers, you can see that german manpower centers should be a priority from a VP point of view, but there are a few other options that i would like to point out:

As you can see, the Hamburg region is an extremely rich target for 43 bombing.
1st, you have 77% of the u-boat factories in the vicinity (red targets), plus, near 20% of all the oil and fuel production for the axis. 20% oil and fuel means 1.44% of the total possible strat bombing targets, just for a 1 hex radius region around Hamburg. Either you play allies or axis, this is definitely an area you want to strat bomb\defend.
Next, the holy Grail of the Axis oil production, the area near Bucharest (check the minimap if your lost)

52% of all the oil production, plus 25% of fuel production. you will need mainland italy airbases to hit these fields, but once you do, you have access to a full 2.66% of the total possible strat bombing targets, plus a big hit to oil production.
Finaly, let me mention this area:

Its near Breslau, meaning deep into polish territory, but in just 2 hexes you have 25% of all the Synthetic fuel production for the Axis, meaning 1.5% of total strat VP points. Worth the shot if you B17 bombers can reach them
As for the German Heavy factories and Manpower centers, the high concentration spots should be easy to pick, and the AI does a good job at it (just set your priorities via Air directive screen). Hope this helps.