Well, you also have to consider the 980X is a 32nm chip where as the 960 is a 45nm chip (not totally sure why that's better).
And the 980X was (and still is) one of the best CPUs around. The 1100T is a good value CPU but not the performance beast that the 980X is. And I think with most things the top of the range products cost more than their performance boost would suggest.
Nvidia 580 vs Nvidia 570 springs to mind as another example.
It really is as simple as that in most cases, you can have a 980x at £400 and a 990x at £450 as a natural progression or, you can price the later at £750, and simply get all the suckers who just have to have the top thing, and make massively more profit.
Anyway, the real way to compare costs is not by mixing value and top end models.
Top quad core from AMD is £130, top hex core is £150, top quad core from Intel is the 2600k at £240, top hex core from Intel is £773.
The cost isn't in manufacturing, quite simple research costs come out of overall profits, the high cost on a 990x and a 980x on launch don't represent trying to claw back R&D costs, in the slightest, they are insanely low volume and don't make the slightest dent in the R&D costs, the overall volume of the hexcore in server parts will be manitudes higher than desktop sales.
Theres simple customers willing to spend £750 on the top chip no matter how much faster it is or how much value it is, there are more "ego" buyers than those who genuinely would see the 133Mhz difference in performance, many many more. If some people will spend twice as much, simply why not price a chip there. Then even completely stupid buyers wouldn't spend £3k on that same chip just because it was faster, there is some limit on sanity but generally speaking the people who would spend 750 on a chip really won't miss £300-400 extra so Intel are happy to have it in their pockets.
In terms of cost a 32nm hexcore is 240mm2, the Nehalem chips it replaced at the top end are 45nm and 296mm2, and a Phenom X4 is 258mm2, competitively sized to 45nm Intel quad cores.
A Sandybridge quad core is 216mm2, so its actually no where near the 2/3rds the size of the hexcore you might expect(of course different architectures) but that would suggest the hexcores should be even closer in price to quad core Sandys(and performance suggests so aswell).
It will effectively cost Intel quite a bit less to produce a £773 selling price 990x, than it costs AMD to produce a £140 quad core Phenom, the consumer should work out if they want to be ripped off quite so much.