Were you spot metering from the brightest part of the clouds, or something else? It may well be that Nikon's metering is set up a little different to Canon, or maybe that your software is not so good at dealing with highlight clipping, or maybe that you are merely metering off the clouds in general and not spot metering off the brightest part of the clouds. If you looked at my album of exposures of the white shirt....
http://picasaweb.google.com/EezyTiger/Exposure?authkey=Gv1sRgCOui54easIX-LQ#
you would note that Lightroom did a great job of recovering blown highlights, even from an exposure at +4, with no real ill-effects. Of course, I wouldn't recommend pushing things that far on purpose. It won't work every time, and I consider it my buffer zone for little surprises, not something to be used on purpose. Metering highlights at up to +3, when shooting raw, is absolutely fine with any of my bodies.
In fact, the review by DPReview of the D3 suggests that it is more than capable of holding details beyond +3 and there is bags of room for highlight recovery. Take a look at this page and especially scroll down the page to the section on raw headroom....
http://www.dpreview.com/reviews/NikonD3/page20.asp
The highlight recovery on that blown out hair is remarkable.
I was shooting at the brightest part of the clouds (waggled the focus point about the cloud until I could not get a lower reading). Then took took shots at 9fps from +1EV in 1/3rd EV increments for 9 frames. Imported into camera raw, then adjusted each frame so that they would reach 1EV. Histograms were virtually identical as you would expect, as were the pictures, until you hit +2 2/3EV where the smallest brightest patches of clouds 'stuck' at pure white, then at +3 bigger patches remained white. They weren't noticable if you weren't pixel peeping, BUT after +3EV then the blues in the sky started turning green (the blue channel was absolutely maxed and the others started to hit the limit too).
Not tried light room myself, perhaps it might fare better as a raw convertor?

